View Filing Data

Basic net income (loss) per share (in dollars per share)

$ 0.02

^[1],[2]

$ 0.00

^[1],[2]

$ (0.09)

^[2]

$ 0.03

^[2]

$ 0.21

^[2]

$ 0.06

^[2]

$ (0.47)

$ (0.52)

$ 0.08

$ (0.72)

$ (0.74)

Net income available to Ionis common stockholders

$ 2,744

$ (976)

$ (11,206)

$ 3,468

$ (5,970)

$ (86,556)

$ (88,278)

$ 2,717

$ (419)

$ 3,468

$ 25,865

$ 7,351

$ 9,661

Shares used in computing basic net income per share (in shares)

124,818

124,370

122,861

121,340

120,989

124,016

120,933

119,719

Income available to Ionis common shareholders, plus assumed conversions

$ 2,717

$ 3,468

$ 25,865

$ 7,351

$ 9,661

Shares issuable related to our ESPP

Shares used in computing diluted net income per share (in shares)

126,862

124,972

123,953

123,378

126,098

120,933

119,719

Diluted net income per share (in dollars per share)

$ 0.02

^[2]

$ 0.00

^[2]

$ (0.09)

^[2]

$ 0.03

^[2],[3]

$ 0.21

^[2],[4]

$ 0.06

^[2],[5]

$ (0.47)

$ (0.52)

$ 0.08

$ (0.72)

$ (0.74)

1 Percent Convertible Senior Notes [Member]

2 3/4 Percent Convertible Senior Notes [Member]

1.00%

2.75%

Stock Options [Member]

Shares issuable related to stock-based compensation (in shares)

1,532

1,674

2,189

2,129

1,619

Restricted Stock Awards [Member]

Shares issuable related to stock-based compensation (in shares)

507

377

403

202

459

Ionis [Member]

$ 18,672

$ 9,168

$ 92,336

Akcea [Member]

Akcea [Member] | Common Stock [Member]

$ (15,955)

$ (9,587)

$ (82,676)

Basic net income (loss) per share (in dollars per share)

45,448

36,556

20,669

$ (0.35)

$ (0.27)

$ (2.82)

Akcea [Member] | Series A Convertible Preferred Stock [Member]

$ (15,955)

$ (9,870)

$ (58,332)

Dividend rate

6.00%

Conversion ratio

converted into common stock on a 1:1 basis

Basic net income (loss) per share (in dollars per share)

5,651

15,748

$ 0.05

$ (1.55)

Accumulated Other Comprehensive Income (Loss) [Roll Forward]

$ 283

$ (24,344)

[1]	As discussed in Note 1, Organization and Significant Accounting Policies, we compute basic net income (loss) per share by dividing the total net income (loss) attributable to our common stockholders by our weighted-average number of common shares outstanding during the period. The calculation of total net income (loss) attributable to our common stockholders for the three months ended December 31, 2017 and September 30, 2017 considered our net income for Ionis on a stand-alone basis plus our share of Akcea's net loss for the periods. To calculate the portion of Akcea's net loss attributable to our ownership, we multiplied Akcea's income (loss) per share by the weighted average shares we owned in Akcea during the period. For the three months ended December 31, 2017, we had net income available to Ionis common stockholders. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during those periods. For the three months ended December 31, 2017, the calculation excluded the 1 percent and 2.75 percent notes because the effect on diluted earnings per share was anti-dilutive. Prior to Akcea's IPO, we owned Akcea series A convertible preferred stock, which included a six percent cumulative dividend. Upon completion of Akcea's IPO in July 2017, our preferred stock was converted into common stock on a 1:1 basis. The preferred stock dividend was not paid at the IPO because it was not a liquidation event or a change in control. During the three months ended September 30, 2017, Akcea used a two-class method to compute its net income (loss) per share because it had both common and preferred shares outstanding during the periods. The two-class method required Akcea to calculate its net income (loss) per share for each class of stock by dividing total distributable losses applicable to preferred and common stock, including the six percent cumulative dividend contractually due to series A convertible preferred shareholders, by the weighted-average of preferred and common shares outstanding during the requisite period. Since Akcea used the two-class method, accounting rules required us to include our portion of Akcea's net income (loss) per share for both Akcea's common and preferred shares which we owned in our calculation of basic and diluted net income (loss) per share for three months ended September 30, 2017. As a result of this calculation, our total net income (loss) available to Ionis common stockholders for the calculation of net income (loss) per share is different than net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders in the consolidated statements of operations.
[2]	We computed net income (loss) per share independently for each of the quarters presented. Therefore, the sum of the quarterly net income (loss) per share will not necessarily equal the total for the year.
[3]	For the three months ended March 31, 2017 we had net income. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during the period. For the three months ended March 31, 2017, the calculation excludes the 1 percent and 2 3/4 percent notes because the effect on diluted earnings per share was anti-dilutive.
[4]	For the three months ended December, 2016, we had net income. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during the period. For the three months ended December 31, 2016, the calculation excludes the 1 percent and 2 3/4 percent notes because the effect on diluted earnings per share would be anti-dilutive.
[5]	For the three months ended September 30, 2016, we had net income. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during the period. For the three months ended September 30, 2016, the calculation excludes the 1 percent and 2 3/4 percent notes because the effect on diluted earnings per share would be anti-dilutive.

Organization and Significant Accounting Policies, Revenue Recognition (Details) $ in Thousands, shares in Millions	1 Months Ended		3 Months Ended			12 Months Ended
	Feb. 28, 2017 USD ($) AccountingUnit	May 31, 2015 USD ($)	Dec. 31, 2017 USD ($) Agreement	Mar. 31, 2017 USD ($) AccountingUnit Drug shares	Jun. 30, 2015 USD ($)	Dec. 31, 2017 USD ($) Drug Category Stage Partner	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Jan. 31, 2017 USD ($)
Revenue Recognition [Abstract]
SPINRAZA royalties						$ 112,540	$ 883	$ 0
Number of categories of milestone events \| Category						3
Number of stages of life-cycle of drugs \| Stage						3
Number of partners that exercised option to license drugs \| Partner						3
Number of drugs licensed under option in collaboration agreements \| Drug						3
Minimum [Member]
Revenue Recognition [Abstract]
Period to complete IND-enabling animal studies						12 months
Period to complete Phase 1 clinical trial						1 year
Period to complete Phase 2 clinical trial						1 year
Period to complete Phase 3 clinical trial						2 years
Period to prepare and submit regulatory filings						6 months
Period to obtain marketing authorization from applicable regulatory agency						1 year
Pre-specified product sales threshold included in commercialization milestones						$ 1,000,000
Maximum [Member]
Revenue Recognition [Abstract]
Period to complete IND-enabling animal studies						18 months
Period to complete Phase 1 clinical trial						2 years
Period to complete Phase 2 clinical trial						3 years
Period to complete Phase 3 clinical trial						4 years
Period to prepare and submit regulatory filings						12 months
Period to obtain marketing authorization from applicable regulatory agency						2 years
Novartis [Member]
Revenue Recognition [Abstract]
Number of agreements \| Agreement			2
Bayer [Member]
Revenue Recognition [Abstract]
Upfront payment received	$ 75,000	$ 100,000			$ 100,000
Bayer [Member]
Revenue Recognition [Abstract]
Payment received for advancing programs	$ 75,000
Number of units of accounting \| AccountingUnit	3
Allocable arrangement consideration	$ 76,300
Consideration allocated to exclusive license	64,900
Consideration allocated to development activities	11,000
Consideration allocated to delivery of API	$ 400
Assumed percentage change in estimated selling price	10.00%
Percentage change in earned revenue based on assumed change in estimated selling price	1.00%
Amount by which earned revenue would change based on assumed change in estimated selling price	$ 700
Novartis [Member]
Revenue Recognition [Abstract]
Number of units of accounting \| AccountingUnit				4
Number of drugs with exclusive option that could be exercised \| Drug				1
Shares issued (in shares) \| shares				1.6
Proceeds from sale of common stock, including premium paid				$ 100,000
Additional amount of common stock required to be purchased				50,000					$ 50,000
Akcea [Member] \| Novartis [Member]
Revenue Recognition [Abstract]
Upfront payment received				$ 75,000
License fee receivable per drug			$ 150,000			$ 150,000

Organization and Significant Accounting Policies, Research, Development and Patent Expenses (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Research, Development and Patent Expenses [Abstract]
Research and development expenses	$ 372.5	$ 340.4	$ 319.5
Patents [Member]
Patents [Abstract]
Estimated useful life	10 years 1 month 6 days
Cost	$ 30.8	28.8
Accumulated amortization	8.8	8.4
Estimated Amortization Expense [Abstract]
2018	1.6
2019	1.4
2020	1.3
2021	1.3
2022	1.2
Patent expenses	2.1	3.9	2.8
Non-cash charges related to write-down	0.4	2.3	1.1
Collaborative Agreements [Member]
Research, Development and Patent Expenses [Abstract]
Research and development expenses	$ 59.5	$ 187.1	$ 161.7

Organization and Significant Accounting Policies, Accrued Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Organization and Significant Accounting Policies [Abstract]
Clincial expenses	$ 16,347	$ 23,428
In-licensing expenses	33,790	6,430
Other miscellanous accruals	16,481	6,155
Total accrued liabilities	$ 66,618	$ 36,013

Organization and Significant Accounting Policies, Noncontrolling Interest in Akcea Therapeutics, Inc. (Details) - USD ($) $ in Thousands	1 Months Ended	5 Months Ended	7 Months Ended	12 Months Ended
	Jul. 31, 2017	Dec. 31, 2017	Jul. 18, 2017	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Akcea IPO [Abstract]
Proceeds from sale of common stock to Novartis in a private placement				$ 50,000	$ 0	$ 0
Investment in subsidiary	$ 25,000
Percentage ownership before IPO			100.00%
Percentage of results included in consolidation			100.00%
Percentage ownership after IPO		68.00%
Akcea [Member]
Akcea IPO [Abstract]
Gross proceeds from IPO	193,800
Proceeds from sale of common stock to Novartis in a private placement	50,000
Net proceeds from IPO	$ 182,400

Organization and Significant Accounting Policies, Cash, Cash Equivalents and Short-Term Investments (Details)	Dec. 31, 2017 Company
Cash, Cash Equivalents and Investments [Abstract]
Number of publicly-held companies in which there is an equity ownership interest of less than 20%	1
Number of privately-held companies in which there is an equity ownership interest of less than 20%	5

Organization and Significant Accounting Policies, Inventory Valuation (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Inventory Valuation [Abstract]
Inventory write-off	$ 0	$ 0	$ 0
Inventories	$ 9,982	$ 7,489

Organization and Significant Accounting Policies, Property, Plant and Equipment (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Property, Plant and Equipment [Abstract]
Less accumulated depreciation	$ (87,676)	$ (80,075)
Property, plant and equipment, net	121,907	92,845
Property, Plant and Equipment, Excluding Land [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	195,090	162,722
Property, plant and equipment, net	107,414	82,647
Computer Software, Laboratory, Manufacturing and Other Equipment [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	$ 66,558	63,287
Computer Software, Laboratory, Manufacturing and Other Equipment [Member] \| Minimum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	3 years
Computer Software, Laboratory, Manufacturing and Other Equipment [Member] \| Maximum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	10 years
Building, Building Improvements and Building Systems [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	$ 92,770	48,909
Building, Building Improvements and Building Systems [Member] \| Minimum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	15 years
Building, Building Improvements and Building Systems [Member] \| Maximum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	40 years
Land Improvements [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	$ 2,853	2,853
Estimated useful lives	20 years
Leasehold Improvements [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	$ 26,748	41,736
Leasehold Improvements [Member] \| Minimum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	5 years
Leasehold Improvements [Member] \| Maximum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	15 years
Furniture and Fixtures [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	$ 6,161	5,937
Furniture and Fixtures [Member] \| Minimum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	5 years
Furniture and Fixtures [Member] \| Maximum [Member]
Property, Plant and Equipment [Abstract]
Estimated useful lives	10 years
Land [Member]
Property, Plant and Equipment [Abstract]
Property, plant and equipment	$ 14,493	$ 10,198

Organization and Significant Accounting Policies, Long-Lived Assets (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Long-Lived Assets [Abstract]
Charges related to write-down of intangible assets	$ 0.8	$ 2.3	$ 1.9

Organization and Significant Accounting Policies, Stock-based Compensation Expense (Details)	12 Months Ended
	Dec. 31, 2017
RSUs [Member]
Stock-Based Compensation [Abstract]
Vesting period	4 years

Organization and Significant Accounting Policies, Accumulated Other Comprehensive Income (Loss) (Details) - USD ($)
$ in Thousands

12 Months Ended

Dec. 31, 2017

Dec. 31, 2016

Dec. 31, 2015

Net other comprehensive loss for the period

$ 99,565

$ 200,790

$ 257,780

(1,401)

(16,793)

(53,312)

Income tax expense included in other comprehensive income

418,719

99,565

200,790

Accumulated Other Comprehensive (Loss) Income [Member]

Accumulated Other Comprehensive Income (Loss) [Roll Forward]

(30,358)

(13,565)

39,747

Unrealized Losses on Securities [Member]

(31,759)

(30,358)

(13,565)

Accumulated Other Comprehensive Income (Loss) [Roll Forward]

Other comprehensive loss before reclassifications, net of tax

^[1]

(960)

(17,219)

(33,101)

Amounts reclassified from accumulated other comprehensive (loss) income

^[2]

(374)

447

(20,211)

Currency Translation Adjustment [Member]

Accumulated Other Comprehensive Income (Loss) [Roll Forward]

Other comprehensive loss before reclassifications, net of tax

$ (67)

$ (21)

$ 0

[1]	There was no tax expense for other comprehensive loss for the years ended December 31, 2017, 2016 or 2015.
[2]	Amounts for 2015 are included in the separate line called "Gain on investment in Regulus Therapeutics Inc." on our Consolidated Statement of Operations.

Organization and Significant Accounting Policies, Convertible Debt (Details)	Dec. 31, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Dec. 31, 2015
1 Percent Convertible Senior Notes [Member]
Convertible Debt [Abstract]
Interest rate on convertible senior notes	1.00%	1.00%	1.00%	1.00%	1.00%
2 3/4 Percent Convertible Senior Notes [Member]
Convertible Debt [Abstract]
Interest rate on convertible senior notes	2.75%	2.75%	2.75%	2.75%	2.75%

Organization and Significant Accounting Policies, Segment Information (Details) - Segment	5 Months Ended	7 Months Ended	12 Months Ended
	Dec. 31, 2017	Jul. 18, 2017	Dec. 31, 2017
Segment Information [Abstract]
Number of operating segments			2
Percentage ownership before IPO		100.00%
Percentage ownership after IPO	68.00%

Organization and Significant Accounting Policies, Fair Value Measurements on a Recurring Basis (Details) - USD ($)
$ in Thousands

Dec. 31, 2017

Dec. 31, 2016

Organization and Significant Accounting Policies [Abstract]

Transfers from Level 1 to Level 2

$ 0

Transfers from Level 2 to Level 1

592,211

Recurring Basis [Member]

Investment in Regulus Therapeutics Inc.

Cash equivalents

^[1]

86,262

54,137

2,414

Recurring Basis [Member] | Corporate Debt Securities [Member]

994,798

646,348

Recurring Basis [Member] | Corporate Debt Securities [Member] | Cash and Cash Equivalents [Member]

647,461

^[2]

396,221

^[3]

Recurring Basis [Member] | Debt Securities issued by U.S. Government Agencies [Member]

11,900

Recurring Basis [Member] | Debt Securities issued by the U.S. Treasury [Member]

^[3]

136,325

55,179

Recurring Basis [Member] | Debt Securities issued by the U.S. Treasury [Member] | Cash and Cash Equivalents [Member]

^[3]

30,818

29,286

Recurring Basis [Member] | Debt Securities issued by States of the U.S. and Political Subdivisions of the States [Member]

3,500

9,300

Recurring Basis [Member] | Quoted Prices in Active Markets (Level 1) [Member]

93,932

^[4]

109,111

^[5]

Investment in Regulus Therapeutics Inc.

Cash equivalents

86,262

54,137

2,414

Recurring Basis [Member] | Quoted Prices in Active Markets (Level 1) [Member] | Corporate Debt Securities [Member]

117,080

85,837

Recurring Basis [Member] | Quoted Prices in Active Markets (Level 1) [Member] | Debt Securities issued by U.S. Government Agencies [Member]

Recurring Basis [Member] | Quoted Prices in Active Markets (Level 1) [Member] | Debt Securities issued by the U.S. Treasury [Member]

Recurring Basis [Member] | Quoted Prices in Active Markets (Level 1) [Member] | Debt Securities issued by States of the U.S. and Political Subdivisions of the States [Member]

30,818

29,286

Recurring Basis [Member] | Significant Other Observable Inputs (Level 2) [Member]

Investment in Regulus Therapeutics Inc.

Cash equivalents

Recurring Basis [Member] | Significant Other Observable Inputs (Level 2) [Member] | Corporate Debt Securities [Member]

877,718

560,511

Recurring Basis [Member] | Significant Other Observable Inputs (Level 2) [Member] | Debt Securities issued by U.S. Government Agencies [Member]

647,461

396,221

Recurring Basis [Member] | Significant Other Observable Inputs (Level 2) [Member] | Debt Securities issued by the U.S. Treasury [Member]

136,325

55,179

Recurring Basis [Member] | Significant Other Observable Inputs (Level 2) [Member] | Debt Securities issued by States of the U.S. and Political Subdivisions of the States [Member]

Recurring Basis [Member] | Significant Unobservable Inputs (Level 3) [Member]

93,932

109,111

$ 0

[1]	Included in cash and cash equivalents on our consolidated balance sheet.
[2]	$11.9 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.
[3]	Included in short-term investments on our consolidated balance sheet.
[4]	$3.5 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.
[5]	$9.3 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.

Organization and Significant Accounting Policies, Fair Value Measurements - Novartis Future Stock Purchase (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Mar. 31, 2017	Jan. 31, 2017
Novartis [Member]
Novartis Future Stock Purchase [Abstract]
Additional amount of common stock required to be purchased		$ 50,000	$ 50,000
Fair value of potential future premium			$ 5,000
Equity Securities [Member]
Unobservable Inputs (Level 3) [Roll Forward]
Beginning balance of Level 3 instruments	$ 0
Value of the potential premium we will receive from Novartis at inception of the SPA (January 2017)	5,035
Write-off of premium to other expenses	(5,035)
Ending balance of Level 3 instruments	$ 0

Organization and Significant Accounting Policies, Income Taxes (Details)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Income Taxes [Abstract]
U.S. federal corporate tax rate		35.00%	35.00%	35.00%
Plan [Member]
Income Taxes [Abstract]
U.S. federal corporate tax rate	21.00%

Organization and Significant Accounting Policies, Impact of Recently Issued Accounting Standards (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Impact of Recently Issued Accounting Standards [Abstract]
Revenue	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Accumulated deficit	(1,187,398)				(1,181,428)				(1,187,398)	(1,181,428)
Income tax expense									(5,980)	2,934	372
Biogen [Member]
Impact of Recently Issued Accounting Standards [Abstract]
Milestone payment earned									50,000
Revenue									259,800	207,900	$ 106,200
Deferred revenue	69,300				$ 67,500				69,300	67,500
Biogen [Member] \| IONIS-MAPT [Member]
Impact of Recently Issued Accounting Standards [Abstract]
Milestone payment earned									10,000
Revenue									10,000
Recognition of Revenue from Customers [Member] \| Plan [Member]
Impact of Recently Issued Accounting Standards [Abstract]
Revenue									17,000	27,000
Deferred revenue	39,000								39,000
Accumulated deficit	$ 39,000								39,000
Income tax expense									$ 0	$ 0

Investments, Contract Maturity of Available-for-Sale Securities (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2017 USD ($) Company	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Contract Maturity of Available-for-Sale Securities [Abstract]
One year or less	71.00%
After one year but within two years	23.00%
After two years but within three and a half years	6.00%
Total	100.00%
Percentage of available-for-sale securities with a maturity of less than two years	94.00%
Maximum contract maturity period, range 1	1 year
Maximum contract maturity period, range 2	2 years
Maximum contract maturity period, range 3	3 years 6 months
Ownership Interests in Private and Public Companies [Abstract]
Number of privately-held companies in which there is an equity ownership interest of less than 20%	5
Number of publicly-held companies in which there is an equity ownership interest of less than 20%	1
Gain on investment in Regulus Therapeutics Inc. \| $	$ 374	$ 0	$ 20,211

Investments, Summary of Investments (Details) - USD ($)
$ in Thousands

Dec. 31, 2017

Dec. 31, 2016

$ 593,872

348

(2,009)

Securities with Maturity of One Year or Less [Member]

592,211

^[1]

$ 643,193

323,708

(1,103)

(319)

Securities with Maturity of More than One Year [Member]

642,096

323,418

^[1]

268,401

268,031

(1,969)

(1,690)

Available-for-sale Securities [Member]

266,440

266,379

^[1]

911,594

591,739

(3,072)

(2,009)

Corporate Debt Securities [Member] | Securities with Maturity of One Year or Less [Member]

908,536

589,797

^[1]

500,599

^[2]

195,087

(752)

(161)

Corporate Debt Securities [Member] | Securities with Maturity of More than One Year [Member]

499,849

194,951

^[1]

148,663

202,408

(1,059)

(1,174)

Debt Securities issued by U.S. Government Agencies [Member] | Securities with Maturity of One Year or Less [Member]

147,612

201,270

^[1]

83,926

26,548

(212)

(10)

Debt Securities issued by U.S. Government Agencies [Member] | Securities with Maturity of More than One Year [Member]

83,714

26,538

^[1]

52,779

28,807

(168)

(167)

Debt Securities issued by the U.S. Treasury [Member] | Securities with Maturity of One Year or Less [Member]

52,611

28,641

^[1]

29,428

29,298

(17)

(14)

Debt Securities issued by the U.S. Treasury [Member] | Securities with Maturity of More than One Year [Member]

29,411

29,286

^[1]

1,409

(2)

Debt Securities issued by States of the U.S. and Political Subdivisions of the States [Member] | Securities with Maturity of One Year or Less [Member]

1,407

^[1],[2]

29,240

72,775

(122)

(134)

Debt Securities issued by States of the U.S. and Political Subdivisions of the States [Member] | Securities with Maturity of More than One Year [Member]

29,122

72,643

^[1]

65,550

36,816

(740)

(349)

Equity Securities [Member]

$ 64,810

36,468

2,133

281

Regulus Therapeutics Inc. [Member]

2,414

2,133

281

Collaborative Arrangement and Licensing Agreement [Abstract]

$ 2,414

[1]	Our available-for-sale securities are held at amortized cost.
[2]	Includes investments classified as cash equivalents on our consolidated balance sheet.

Investments, Investments Temporarily Impaired (Details) $ in Thousands	Dec. 31, 2017 USD ($) Investment
Temporarily Impaired Investments [Abstract]
Number of investments \| Investment	588
Estimated fair value, less than 12 months of temporary impairment	$ 752,571
Unrealized losses, less than 12 months of temporary impairment	(2,062)
Estimated fair value, more than 12 months of temporary impairment	127,097
Unrealized losses, more than 12 months of temporary impairment	(1,010)
Estimated fair value, total temporary impairment	879,668
Unrealized losses, total temporary impairment	$ (3,072)
Corporate Debt Securities [Member]
Temporarily Impaired Investments [Abstract]
Number of investments \| Investment	476
Estimated fair value, less than 12 months of temporary impairment	$ 551,446
Unrealized losses, less than 12 months of temporary impairment	(1,236)
Estimated fair value, more than 12 months of temporary impairment	74,987
Unrealized losses, more than 12 months of temporary impairment	(575)
Estimated fair value, total temporary impairment	626,433
Unrealized losses, total temporary impairment	$ (1,811)
Debt Securities issued by U.S. Government Agencies [Member]
Temporarily Impaired Investments [Abstract]
Number of investments \| Investment	45
Estimated fair value, less than 12 months of temporary impairment	$ 107,788
Unrealized losses, less than 12 months of temporary impairment	(262)
Estimated fair value, more than 12 months of temporary impairment	27,538
Unrealized losses, more than 12 months of temporary impairment	(118)
Estimated fair value, total temporary impairment	135,326
Unrealized losses, total temporary impairment	$ (380)
Debt Securities issued by the U.S. Treasury [Member]
Temporarily Impaired Investments [Abstract]
Number of investments \| Investment	7
Estimated fair value, less than 12 months of temporary impairment	$ 30,818
Unrealized losses, less than 12 months of temporary impairment	(19)
Estimated fair value, more than 12 months of temporary impairment	0
Unrealized losses, more than 12 months of temporary impairment	0
Estimated fair value, total temporary impairment	30,818
Unrealized losses, total temporary impairment	$ (19)
Debt Securities issued by States of the U.S. and Political Subdivisions of the States [Member]
Temporarily Impaired Investments [Abstract]
Number of investments \| Investment	60
Estimated fair value, less than 12 months of temporary impairment	$ 62,519
Unrealized losses, less than 12 months of temporary impairment	(545)
Estimated fair value, more than 12 months of temporary impairment	24,572
Unrealized losses, more than 12 months of temporary impairment	(317)
Estimated fair value, total temporary impairment	87,091
Unrealized losses, total temporary impairment	$ (862)

Long-Term Obligations and Commitments, Long-Term Obligations (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Long-Term Obligations [Abstract]
Total long-term obligations, including current portion	$ 607,477	$ 589,105
Less: current portion	(1,621)	(1,185)
Total Long-Term Obligations	605,856	587,920
1 Percent Convertible Senior Notes [Member]
Long-Term Obligations [Abstract]
Total long-term obligations, including current portion	533,111	500,511
Long-term Mortgage Debt [Member]
Long-Term Obligations [Abstract]
Total long-term obligations, including current portion	59,771	0
Long-term Financing Liability for Leased Facility [Member]
Long-Term Obligations [Abstract]
Total long-term obligations, including current portion	0	72,359
Fixed Rate Note with Morgan Stanley [Member]
Long-Term Obligations [Abstract]
Total long-term obligations, including current portion	12,500	12,500
Leases and Other Obligations [Member]
Long-Term Obligations [Abstract]
Total long-term obligations, including current portion	$ 2,095	$ 3,735

Long-Term Obligations and Commitments, Convertible Notes (Details) $ / shares in Units, $ in Thousands	1 Months Ended		12 Months Ended
	Dec. 31, 2016 USD ($)	Nov. 30, 2014 USD ($)	Dec. 31, 2017 USD ($) shares $ / shares	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Mar. 31, 2017	Sep. 30, 2016
Convertible Notes [Abstract]
Loss on early retirement of debt			$ 0	$ (3,983)	$ 0
Amortization of debt discount and debt issuance costs			32,500	25,100	$ 23,200
Long-term debt	$ 500,511		$ 533,111	$ 500,511
1 Percent Convertible Senior Notes [Member]
Convertible Notes [Abstract]
Maturity date			Nov. 30, 2021
Interest rate	1.00%		1.00%	1.00%	1.00%	1.00%	1.00%
Conversion price per share (in dollars per share) \| $ / shares			$ 66.81
Total shares of common stock subject to conversion (in shares) \| shares			10,300,000
Percentage of principal amount used a purchase price upon occurrence of fundamental change			100.00%
Principal amount of convertible notes outstanding	$ 685,450		$ 685,450	$ 685,450
Unamortized portion of debt discount	175,699		144,112	175,699
Long-term debt	500,511		533,111	500,511
Carrying value of equity component	219,011		219,011	219,011
1 Percent Convertible Senior Notes [Member] \| Level 2 [Member]
Convertible Notes [Abstract]
Fair value of outstanding notes	700,969		$ 727,420	700,969
1 Percent Convertible Senior Notes Issued in November 2014 [Member]
Convertible Notes [Abstract]
Face amount of offering		$ 500,000
Proceeds from issuance of 1 percent convertible senior notes, net of issuance costs		487,000
Issue date			Nov. 30, 2014
Nonconvertible debt borrowing rate			7.40%
Effective interest rate			7.80%
Amortization period of debt discount			7 years
1 Percent Convertible Senior Notes Issued in December 2016 [Member]
Convertible Notes [Abstract]
Face amount of offering	185,500			185,500
Issue date			Dec. 31, 2016
Nonconvertible debt borrowing rate			6.80%
Effective interest rate			7.20%
Amortization period of debt discount			5 years
2 3/4 Percent Convertible Senior Notes [Member]
Convertible Notes [Abstract]
Principal amount repurchased	61,100	140,000		$ 61,100
Repurchase of convertible senior notes		441,900
Loss on early retirement of debt	$ 3,983
Interest rate	2.75%		2.75%	2.75%	2.75%	2.75%	2.75%
Principal amount of convertible notes outstanding		$ 61,200

Long-Term Obligations and Commitments, Financing Arrangements (Details) $ in Millions	12 Months Ended
	Dec. 31, 2017 USD ($)
Fixed Rate Note with Morgan Stanley [Member]
Financing Arrangements [Abstract]
Outstanding borrowings	$ 12.5
Interest rate	2.31%
Maturity date	Sep. 30, 2019
Morgan Stanley [Member] \| Revolving Line of Credit [Member]
Financing Arrangements [Abstract]
Term of agreement	5 years
Maximum borrowing capacity	$ 30.0
Commitment fee percentage on unused capacity	0.25%
Morgan Stanley [Member] \| Revolving Line of Credit [Member] \| LIBOR [Member]
Financing Arrangements [Abstract]
Term of variable rate	1 month
Basis spread on variable rate	1.25%
Term of fixed rate elected	one, two, three, four, six, or twelve months

Long-Term Obligations and Commitments, Research and Development and Manufacturing Facilities (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended	12 Months Ended
	Jul. 31, 2017	Sep. 30, 2017	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Research and Development and Manufacturing Facilities [Abstract]
Loss on extinguishment of financing liability for leased facility			$ (7,689)	$ 0	$ 0
Primary R&D Facility [Member]
Research and Development and Manufacturing Facilities [Abstract]
Payment to acquire building	$ 79,400
Loss on extinguishment of financing liability for leased facility		$ (7,689)
Proceeds from mortgage loan	$ 51,300
Interest rate	3.88%
Period to make interest only payments on mortgage loan			5 years
Manufacturing Facility [Member]
Research and Development and Manufacturing Facilities [Abstract]
Payment to acquire building	$ 14,000
Proceeds from mortgage loan	$ 9,100
Interest rate	4.20%
Period to make interest only payments on mortgage loan			5 years

Long-Term Obligations and Commitments, Maturity Schedules (Details) - USD ($) $ in Thousands	Dec. 31, 2017	Dec. 31, 2016
Annual Debt and Other Obligation Maturities [Abstract]
Less: current portion	$ (1,621)	$ (1,185)
Total	605,856	$ 587,920
Long-Term Obligations, Excluding Financing Liability for Leased Facility [Member]
Annual Debt and Other Obligation Maturities [Abstract]
2018	9,617
2019	22,082
2020	9,330
2021	694,774
2022	2,809
Thereafter	71,603
Total minimum payments	810,215
Less: current portion	(53)
Less: fixed and determinable interest	(51,465)
Less: unamortized portion of debt discount	(144,791)
Plus: Deferred rent	165
Total	$ 614,071

Long-Term Obligations and Commitments, Operating Leases (Details) - Office and Laboratory Space [Member] $ in Thousands	12 Months Ended
	Dec. 31, 2017 USD ($) Option	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Annual Future Minimum Payments Under Operating Leases [Abstract]
2018	$ 864
2019	636
2020	477
2021	147
Total minimum payments	2,124
Rent expense	1,700	$ 2,000	$ 2,000
Deferred rent	$ 100	$ 2,100
Building [Member]
Operating Leases [Abstract]
Number of options to extend lease \| Option	2
Term of lease extension	5 years

Stockholders' Equity, Preferred and Common Stock (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Common Stock [Abstract]
Common stock, shares authorized to issue (in shares)	300,000,000	300,000,000
Common stock, shares issued (in shares)	124,976,373	121,636,273
Common stock, shares outstanding (in shares)	124,976,373	121,636,273
Net proceeds from stock option exercises, vesting of restricted stock units, and ESPP purchases	$ 22,931	$ 13,417	$ 24,888
Preferred Stock [Member]
Preferred Stock [Abstract]
Preferred stock, shares authorized (in shares)	15,000,000
Preferred stock, shares outstanding (in shares)	0
Series C Junior Participating Preferred Stock [Member]
Preferred Stock [Abstract]
Preferred stock, shares issued (in shares)	0
Preferred stock, shares outstanding (in shares)	0
Common Stock [Member]
Common Stock [Abstract]
Common stock, shares authorized to issue (in shares)	300,000,000	300,000,000
Common stock, shares issued (in shares)	124,976,373	121,636,273
Common stock, shares outstanding (in shares)	124,973,373	121,636,273
Common shares reserved for future issuance (in shares)	18,419,727
Number of shares issued for stock option exercises, vesting of restricted stock units, and ESPP purchases (in shares)	1,706,000	1,285,000	1,908,000
Net proceeds from stock option exercises, vesting of restricted stock units, and ESPP purchases	$ 22,900	$ 13,700	$ 24,900

Stockholders' Equity, Stock Plans (Details)	1 Months Ended	12 Months Ended
Stockholders' Equity, Stock Plans (Details)	Jun. 30, 2009 shares	Dec. 31, 2017 Installment $ / shares shares	May 31, 2017 shares	Apr. 30, 2017 shares	Dec. 31, 2016 shares	Jun. 30, 2015 shares	May 31, 2015 shares
Stock Options [Member]
Stock Plans [Abstract]
Number of options outstanding (in shares)		9,397,000			9,178,000
Number of options exercisable (in shares)		5,182,000
Restricted Stock Units [Member]
Stock Plans [Abstract]
Vesting period		4 years
1989 Stock Option Plan [Member]
Stock Plans [Abstract]
Number of shares authorized (in shares)		20,000,000
Vesting period		4 years
Award term		7 years
Number of options outstanding (in shares)		1,603,403
Number of options exercisable (in shares)		1,553,252
Number of shares available for grant (in shares)		31,878
1989 Stock Option Plan [Member] \| One Year from Date of Grant [Member]
Stock Plans [Abstract]
Vesting percentage		25.00%
2011 Equity Incentive Plan [Member]
Stock Plans [Abstract]
Number of shares authorized (in shares)			16,000,000	11,000,000		11,000,000	5,500,000
Number of options outstanding (in shares)		7,120,643
Number of options exercisable (in shares)		3,201,717
Number of shares available for grant (in shares)		6,822,389
Number of awards outstanding (in shares)		821,771
2011 Equity Incentive Plan [Member] \| Stock Options [Member] \| Minimum [Member]
Stock Plans [Abstract]
Vesting period		2 years
2011 Equity Incentive Plan [Member] \| Restricted Stock Units [Member]
Stock Plans [Abstract]
Vesting period		4 years
2011 Equity Incentive Plan [Member] \| Restricted Stock Units [Member] \| Minimum [Member]
Stock Plans [Abstract]
Vesting period		3 years
2002 Non-Employee Directors' Stock Option Plan [Member]
Stock Plans [Abstract]
Number of shares authorized (in shares)						2,000,000	1,200,000
Award term		10 years
Number of options outstanding (in shares)		672,750
Number of options exercisable (in shares)		427,125
Number of shares available for grant (in shares)		635,867
Number of awards outstanding (in shares)		40,933
2002 Non-Employee Directors' Stock Option Plan [Member] \| One Year from Date of Grant [Member]
Stock Plans [Abstract]
Number of equal annual installments over which options become exercisable \| Installment		4
Employee Stock Purchase Plan [Member]
Stock Plans [Abstract]
Number of shares authorized (in shares)		3,524,596
Number of shares available for grant (in shares)		668,232
Number of additional shares reserved for issuance (in shares)	150,000	150,000
Maximum percentage of employee compensation used to purchase shares		10.00%
Percentage of fair market value used to determine purchase price of stock		85.00%
Purchase period		6 months
Holding period for purchased stock		6 months
Shares purchased and issued under ESPP (in shares)		67,481
Purchase price (in dollars per share) \| $ / shares		$ 27.51

Stockholders' Equity, Stock Option Activity (Details) - Stock Options [Member] - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Number of Shares [Abstract]
Outstanding at beginning of period (in shares)	9,178
Granted (in shares)	3,274
Exercised (in shares)	(1,345)
Cancelled/forfeited/expired (in shares)	(1,710)
Outstanding at end of period (in shares)	9,397	9,178
Exercisable at end of period (in shares)	5,182
Weighted Average Exercise Price Per Share [Abstract]
Outstanding at beginning of period (in dollars per share)	$ 40.48
Granted (in dollars per share)	47.76
Exercised (in dollars per share)	15.74
Cancelled/forfeited/expired (in dollars per share)	51.71
Outstanding at end of period (in dollars per share)	44.52	$ 40.48
Exercisable at end of period (in dollars per share)	$ 39.10
Average Remaining Contractual Term, Aggregate Intrinsic Value and Other [Abstract]
Average remaining contractual term, outstanding at end of period	4 years 5 months 1 day
Average remaining contractual term, exercisable at end of period	3 years 3 months 29 days
Aggregate intrinsic value, outstanding at end of period	$ 92,288
Aggregate intrinsic value, exercisable at end of period	$ 80,167
Weighted average fair value of options granted (in dollars per share)	$ 25.42	$ 26.72	$ 27.44
Intrinsic value of options exercised	$ 49,500	$ 28,000	$ 84,700
Cash received from exercise of stock options	$ 21,200	$ 12,600	$ 23,600
Weighted-average fair value of options exercised (in dollars per share)	$ 52.53
Unrecognized Compensation Expense [Abstract]
Unrecognized compensation expense related to non-vested stock options	$ 75,200
Weighted average period for recognition	1 year 2 months 12 days

Stockholders' Equity, Restricted Stock Unit Activity (Details) - Restricted Stock Units [Member] - USD ($) $ / shares in Units, shares in Thousands, $ in Millions	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Number of Shares [Abstract]
Non-vested at beginning of period (in shares)	778
Granted (in shares)	420
Vested (in shares)	(296)
Cancelled/forfeited (in shares)	(39)
Non-vested at end of period (in shares)	863	778
Weighted Average Grant Date Fair Value per Share [Abstract]
Non-vested at beginning of period (in dollars per share)	$ 47.68
Granted (in dollars per share)	48.88	$ 41.79	$ 65.69
Vested (in dollars per share)	43.79
Cancelled/forfeited (in dollars per share)	48.90
Non-vested at end of period (in dollars per share)	$ 49.55	$ 47.68
Unrecognized Compensation Expense [Abstract]
Unrecognized compensation cost related to non-vested RSUs	$ 16.5
Weighted average period for recognition	1 year 2 months 12 days

Stockholders' Equity, Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Stock-Based Compensation [Abstract]
Stock-based compensation expense	$ 85,975	$ 72,108	$ 59,314
Research, Development and Patent [Member]
Stock-Based Compensation [Abstract]
Stock-based compensation expense	64,521	55,099	43,638
Selling, General and Administrative [Member]
Stock-Based Compensation [Abstract]
Stock-based compensation expense	21,454	17,009	15,676
Akcea Therapeutics [Member]
Stock-Based Compensation [Abstract]
Stock-based compensation expense	$ 17,500	$ 10,100	$ 6,500

Stockholders' Equity, Stock-based Valuation Information (Details)	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Employee Stock Options [Member]
Weighted-Average Assumptions [Abstract]
Risk-free interest rate	1.80%	1.50%	1.50%
Dividend yield	0.00%	0.00%	0.00%
Volatility	65.90%	58.70%	53.80%
Expected life	4 years 6 months	4 years 6 months	4 years 6 months
Board of Director Stock Options [Member]
Weighted-Average Assumptions [Abstract]
Risk-free interest rate	2.20%	1.30%	2.10%
Dividend yield	0.00%	0.00%	0.00%
Volatility	61.20%	53.10%	52.20%
Expected life	6 years 7 months 6 days	6 years 6 months	6 years 10 months 24 days
Employee Stock Purchase Plan (ESPP) [Member]
Weighted-Average Assumptions [Abstract]
Risk-free interest rate	0.80%	0.40%	0.10%
Dividend yield	0.00%	0.00%	0.00%
Volatility	59.90%	86.40%	51.70%
Expected life	6 months	6 months	6 months

Income Taxes, Loss Before Income Tax (Benefit) Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Income Taxes [Abstract]
United States	$ (11,802)	$ (83,622)	$ (87,906)
Foreign	(11,474)	0	0
Loss before income tax benefit (expense)	$ (23,276)	$ (83,622)	$ (87,906)

Income Taxes, Income Tax (Benefit) Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Current [Abstract]
Federal	$ (7,460)	$ 1,067	$ 379
State	1,246	1,867	(7)
Foreign	234	0	0
Total current income tax (benefit) expense	(5,980)	2,934	372
Deferred [Abstract]
Federal	0	0	0
State	0	0	0
Total deferred income tax (benefit) expense	0	0	0
Income tax (benefit) expense	$ (5,980)	$ 2,934	$ 372

Income Taxes, Reconciliation of Statutory to Effective Tax Rate (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Reconciliation Between Effective and Statutory Tax Rate [Abstract]
Pre-tax loss	$ (23,276)	$ (83,622)	$ (87,906)
Statutory rate	(8,147)	(29,268)	(30,767)
State income tax net of federal benefit	722	(276)	1
Foreign	4,299	0	0
Net change in valuation allowance	(76,409)	55,927	69,499
Net operating loss expiration	3,987	0	0
Tax credits	(32,769)	(26,954)	(41,284)
Deferred tax true-up	4,848	2,591	1,496
Tax Cuts and Jobs Act	107,323	0	0
Nondeductible items	4,123	1,149	1,055
Akcea deconsolidation adjustment at IPO	469	0	0
Excess stock-based compensation	(14,337)	0	0
Other	(89)	(235)	372
Income tax (benefit) expense	$ (5,980)	$ 2,934	$ 372
Reconciliation Between Effective and Statutory Tax Rate Percentage [Abstract]
Statutory rate	35.00%	35.00%	35.00%
State income tax net of federal benefit	(3.10%)	0.30%	0.00%
Foreign	(18.30%)	0.00%	0.00%
Net change in valuation allowance	328.30%	(66.90%)	(79.10%)
Net operating loss expiration	(17.00%)	0.00%	0.00%
Tax credits	140.80%	32.20%	47.00%
Deferred tax true-up	(20.60%)	(3.10%)	(1.70%)
Tax Cuts and Jobs Act	(461.10%)	0.00%	0.00%
Nondeductible items	(17.90%)	(1.40%)	(1.20%)
Akcea deconsolidation adjustment at IPO	(2.00%)	0.00%	0.00%
Excess stock-based compensation	61.00%	0.00%	0.00%
Other	0.60%	0.40%	(0.40%)
Effective rate	25.70%	(3.50%)	(0.40%)

Income Taxes, Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Deferred Tax Assets [Abstract]
Net operating loss carryovers	$ 153,575	$ 194,372
R&D credits	240,290	193,845
Deferred revenue	42,055	54,203
Stock-based compensation	40,090	48,209
Intangible and capital assets	672	0
Other	12,164	26,228
Total deferred tax assets	488,846	516,857
Deferred Tax Liabilities [Abstract]
Convertible debt	(32,391)	(62,669)
Intangible and capital assets	0	(2,030)
Net deferred tax asset	456,455	452,158
Valuation allowance	(456,455)	(452,158)
Total net deferred tax assets and liabilities	0	$ 0
Impact of change in tax rate on deferred tax assets under the Tax Act	107,300
Tax benefit related to cumulative prior year AMT tax credit carryovers under the Tax Act	$ (7,700)

Income Taxes, Tax Credit Carryforwards (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Income Taxes [Abstract]
Excess tax benefits from stock-based compensation awards		$ 1,861	$ 396
Deferred Tax Assets [Member]
Income Taxes [Abstract]
Increase in valuation allowance	$ 4,300
Research and Development [Member] \| Federal [Member]
Tax Credit Carryforwards [Abstract]
Tax credit carryforwards	233,300
Research and Development [Member] \| California [Member]
Tax Credit Carryforwards [Abstract]
Tax credit carryforwards	56,200
Federal [Member]
Operating Loss Carryforwards [Abstract]
Net operating loss carryforwards	561,100
California [Member]
Operating Loss Carryforwards [Abstract]
Net operating loss carryforwards	$ 887,100

Income Taxes, Gross Unrecognized Tax Benefits (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Gross Unrecognized Tax Benefits [Roll Forward]
Beginning balance of unrecognized tax benefits	$ 66,999	$ 51,257	$ 27,365
Settlement of prior period tax positions	0	(4,033)	0
Increase for prior period tax positions	1,520	7,928	215
Increase for current period tax positions	9,495	11,847	23,677
Ending balance of unrecognized tax benefits	78,014	$ 66,999	$ 51,257
Unrecognized tax benefits that could impact effective tax rate, if recognized	63,600
Interest and penalties on unrecognized tax benefits	$ 0

Collaborative Arrangements and Licensing Agreements, AstraZeneca (Details) $ in Thousands	1 Months Ended				3 Months Ended								12 Months Ended
	Feb. 27, 2018 USD ($)	Dec. 31, 2016 USD ($)	Jul. 31, 2015 USD ($)	Dec. 31, 2012 USD ($)	Dec. 31, 2017 USD ($) Drug	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($) AccountingUnit Drug Program	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned					$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
AstraZeneca [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Deferred revenue		$ 51,500			41,800				$ 51,500				41,800	51,500
Revenue earned													$ 13,800	$ 64,900	$ 6,400
AstraZeneca [Member] \| Revenue [Member] \| Strategic Partner [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Concentration percentage													3.00%	19.00%	2.00%
Cardiometabolic and Renal Diseases [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront payment received			$ 65,000
Number of units of accounting \| AccountingUnit													1
Minimum potential amount of payments receivable for license fees and substantive milestones					4,000,000								$ 4,000,000
Maximum amount of payments receivable for development milestones					1,100,000								1,100,000
Maximum amount of payments receivable for regulatory milestones					2,900,000								2,900,000
Cumulative payments received					93,000								93,000
Milestone payment earned		$ 25,000
Next prospective milestone					10,000								10,000
Cardiometabolic and Renal Diseases [Member] \| Subsequent Event [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Milestone payment earned	$ 30,000
Oncology [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Minimum potential amount of payments receivable for license fees and substantive milestones					750,000								750,000
Maximum amount of payments receivable for development milestones					226,000								226,000
Maximum amount of payments receivable for regulatory milestones					485,000								485,000
Cumulative payments received					97,800								97,800
Milestone payment earned				$ 11,500
Next prospective milestone					17,500								$ 17,500
Number of drugs that can be licensed under option in collaboration agreement \| Drug													3
Number of anti-cancer research programs covered by collaboration agreement \| Program													3
Cumulative upfront fees received					31,000								$ 31,000
Upfront fee amortized into revenue					11,900								11,900
Deferred revenue					7,600								7,600
Milestone payment to be earned					$ 5,000								$ 5,000
Number of additional drugs that can be developed under research programs covered by collaboration agreement \| Drug					2								2

Collaborative Arrangements and Licensing Agreements, Biogen (Details) $ in Thousands	1 Months Ended			3 Months Ended								12 Months Ended
	Dec. 31, 2017 USD ($) Drug Market	Sep. 30, 2013 USD ($)	Dec. 31, 2012 USD ($) Program Target	Dec. 31, 2017 USD ($) Drug Market	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($) Drug Market	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
SPINRAZA royalties												$ 112,540	$ 883	$ 0
Revenue earned				$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	346,620	283,703
Biogen [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Number of additional drugs in clinical development to treat neurodegenerative diseases \| Drug												6
Cumulative payments received	$ 745,000			745,000								$ 745,000
Cumulative payments received	745,000			745,000								745,000
Revenue earned												259,800	207,900	$ 106,200
Deferred revenue	69,300			69,300				$ 67,500				$ 69,300	$ 67,500
Biogen [Member] \| Revenue [Member] \| Strategic Partner [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Concentration percentage												51.00%	60.00%	37.00%
SPINRAZA [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Cumulative payments received	$ 436,000			$ 436,000								$ 436,000
Number of global markets were SPINRAZA is available \| Market	30			30								30
SPINRAZA royalties												$ 112,540
Milestone payments received												90,000
Cumulative payments received	$ 436,000			$ 436,000								436,000
News Antisense Drugs for Treatment of SMA [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Cumulative payments received	800,000			800,000								800,000
Upfront payment recorded as deferred revenue	25,000
Maximum amount of payments receivable for license fees and substantive milestones	1,200,000			1,200,000								1,200,000
Maximum amount of payments receivable for development milestones	80,000			80,000								80,000
Maximum amount of payments receivable for commercialization milestones	180,000			180,000								180,000
Cumulative payments received	800,000			800,000								$ 800,000
Royalty percentage received on net sales of drug												20.00%
Next prospective milestone	45,000			45,000								$ 45,000
Neurology [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Cumulative payments received	56,000			56,000								56,000
Milestone payments received												10,000
Upfront payment recorded as deferred revenue			$ 30,000
Cumulative payments received	56,000			56,000								56,000
Next prospective milestone	7,500			7,500								7,500
Number of targets \| Target			3
Number of programs under which drugs are to be developed and commercialized \| Program			3
Maximum amount of payments receivable per program for license fee and substantive milestone payments	210,000			210,000								210,000
Maximum amount of payments receivable per program for development milestones	10,000			10,000								10,000
Maximum amount of payments receivable per program for regulatory milestones	130,000			130,000								130,000
Strategic Neurology [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Cumulative payments received	165,400			165,400								165,400
Milestone payments received												15,000
Upfront payment recorded as deferred revenue		$ 100,000
Cumulative payments received	165,400			165,400								165,400
Next prospective milestone	$ 10,000			$ 10,000								$ 10,000
Number of drugs currently being advanced \| Drug	5			5								5
Term of collaboration agreement												6 years
Strategic Neurology [Member] \| Antisense Molecule [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Maximum amount of payments receivable for license fees and substantive milestones	$ 260,000			$ 260,000								$ 260,000
Maximum amount of payments receivable for development milestones	60,000			60,000								60,000
Maximum amount of payments receivable for regulatory milestones	130,000			130,000								130,000
Strategic Neurology [Member] \| Other Modalities [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Maximum amount of payments receivable for license fees and substantive milestones	90,000			90,000								90,000
Maximum amount of payments receivable for development milestones	35,000			35,000								35,000
Maximum amount of payments receivable for regulatory milestones	$ 55,000			$ 55,000								$ 55,000

Collaborative Arrangements and Licensing Agreements, Bayer (Details) - USD ($) $ in Thousands	1 Months Ended			3 Months Ended									12 Months Ended
	Feb. 28, 2017	Jun. 30, 2015	May 31, 2015	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Jun. 30, 2015	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned				$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874		$ 507,666	$ 346,620	$ 283,703
Bayer [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront payment received	$ 75,000		$ 100,000									$ 100,000
Revenue earned	$ 64,900	$ 91,200											69,200	5,400	$ 93,400
Maximum amount of payments receivable for license fees and substantive milestones				385,000									385,000
Maximum amount of payments receivable for development milestones				125,000									125,000
Maximum amount of payments receivable for commercialization milestones				110,000									110,000
Cumulative payments received				175,000									175,000
Next prospective milestone				10,000									10,000
Deferred revenue				$ 7,300				$ 1,400					$ 7,300	$ 1,400
Bayer [Member] \| Revenue [Member] \| Strategic Partner [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Concentration percentage													14.00%	2.00%	33.00%
Bayer [Member] \| Minimum [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Royalty percentage received on gross margins of both drugs combined													20.00%

Collaborative Arrangements and Licensing Agreements, GSK (Details) $ in Thousands	1 Months Ended	3 Months Ended								12 Months Ended
	Mar. 31, 2010 USD ($)	Dec. 31, 2017 USD ($) Drug	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($) Drug	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned		$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
GSK [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Number of drugs currently being advanced \| Drug		2								2
Cumulative payments received		$ 162,000								$ 162,000
Upfront payment received	$ 38,000
Maximum amount of payments receivable for license fees and substantive milestones		262,000								262,000
Maximum amount of payments receivable for development milestones		47,500								47,500
Maximum amount of payments receivable for regulatory milestones		120,000								120,000
Maximum amount of payments receivable for commercialization milestones		70,000								70,000
Next prospective milestone		$ 15,000								15,000
Revenue earned										$ 8,600	12,300	$ 33,300
Deferred revenue						$ 2,100					$ 2,100
GSK [Member] \| Revenue [Member] \| Strategic Partner [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Concentration percentage										2.00%	4.00%	12.00%

Collaborative Arrangements and Licensing Agreements, Janssen Biotech, Inc. (Details) $ in Thousands	1 Months Ended		3 Months Ended								12 Months Ended			24 Months Ended
	Jan. 31, 2018 USD ($)	Dec. 31, 2014 USD ($)	Dec. 31, 2017 USD ($)	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($) Program	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2017 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned			$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Janssen Biotech, Inc. [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Number of programs under which drugs are to be developed and commercialized \| Program											3
Upfront payment recorded as deferred revenue		$ 35,000
Minimum amount of payments receivable for license fees and substantive milestones			800,000								$ 800,000			$ 800,000
Maximum amount of payments receivable for development milestones			175,000								175,000			175,000
Maximum amount of payments receivable for regulatory milestones			440,000								440,000			440,000
Maximum amount of payments receivable for commercialization milestones			180,000								180,000			180,000
Cumulative payments received			61,800								61,800			61,800
License fee received														15,000
Next prospective milestone			$ 5,000								5,000			$ 5,000
Revenue earned											$ 33,500	27,300	$ 8,900
Deferred revenue							$ 17,500					$ 17,500
Janssen Biotech, Inc. [Member] \| Subsequent Event [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Payment received for advancing programs	$ 5,000

Collaborative Arrangements and Licensing Agreements, Novartis (Details) $ in Thousands, shares in Millions	3 Months Ended								12 Months Ended
	Dec. 31, 2017 USD ($)	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($) AccountingUnit shares	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Jan. 31, 2017 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Novartis [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Shares issued (in shares) \| shares				1.6
Proceeds from sale of common stock, including premium paid				$ 100,000
Additional amount of common stock required to be purchased				$ 50,000								$ 50,000
Number of units of accounting \| AccountingUnit				4
Total consideration under collaboration				$ 180,000
Premium received on shares issued				28,400
Potential premium received if common stock is purchased in the future at a premium				5,000
Consideration allocated to equity				71,600
Consideration allocated to development services and delivery of API for AKCEA-APO(a)-L and AKCEA-APOCIII-L				108,400
Revenue earned									55,200
Deferred revenue	58,900								$ 58,900
Novartis [Member] \| Revenue [Member] \| Strategic Partner [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Concentration percentage									11.00%
Akcea [Member] \| Novartis [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront payment received				75,000
Portion of upfront payment retained				60,000
Portion of upfront payment paid as a sublicense fee				$ 15,000
License fee receivable per drug	150,000								$ 150,000
Next prospective milestone	25,000								$ 25,000
Percentage of license fees, milestone payments and royalties paid as sublicense fee									50.00%
Akcea [Member] \| Novartis [Member] \| AKCEA-APO(a)-L [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Maximum amount of payments receivable for milestones	600,000								$ 600,000
Maximum amount of payments receivable for development milestones	25,000								25,000
Maximum amount of payments receivable for regulatory milestones	290,000								290,000
Maximum amount of payments receivable for commercialization milestones	285,000								$ 285,000
Royalty percentage received on sales of drug									20.00%
Consideration allocated to development activities	64,000								$ 64,000
Consideration allocated to delivery of API	1,500								1,500
Akcea [Member] \| Novartis [Member] \| AKCEA-APOCIII-L [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Maximum amount of payments receivable for milestones	530,000								530,000
Maximum amount of payments receivable for development milestones	25,000								25,000
Maximum amount of payments receivable for regulatory milestones	240,000								240,000
Maximum amount of payments receivable for commercialization milestones	265,000								$ 265,000
Royalty percentage received on sales of drug									20.00%
Consideration allocated to development activities	40,100								$ 40,100
Consideration allocated to delivery of API	$ 2,800								$ 2,800

Collaborative Arrangements and Licensing Agreements, Roche (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended								12 Months Ended
	Jan. 31, 2018	Apr. 30, 2013	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned			$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Roche [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront payment recorded as deferred revenue		$ 30,000
Milestone payments received											3,000
Maximum amount of payments receivable for license fees and substantive milestones			365,000								365,000
Maximum amount of payments receivable for development milestones			70,000								70,000
Maximum amount of payments receivable for regulatory milestones			170,000								170,000
Maximum amount of payments receivable for commercialization milestones			80,000								80,000
Maximum amount of payment receivable for each additional drug developed			136,500								136,500
Cumulative payments received			60,000								60,000
Next prospective milestone			$ 10,000								10,000
Revenue earned											$ 53,000	7,100	$ 31,200
Deferred revenue							$ 1,700					$ 1,700
Roche [Member] \| Revenue [Member] \| Strategic Partner [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Concentration percentage											10.00%	2.00%	11.00%
Roche [Member] \| Subsequent Event [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
License fee received	$ 45,000

Collaborative Arrangements and Licensing Agreements, Achaogen, Inc. (Details) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017 USD ($)	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($) Drug	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2006 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Achaogen, Inc. [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront fee in the form of equity securities												$ 1,500
Number of drugs to be developed and commercialized \| Drug									2
Maximum amount of payments receivable for development, regulatory and commercialization milestones	49,300								$ 49,300
Cumulative payments received	7,000								7,000
Next prospective milestone	$ 7,500								7,500
Revenue earned									$ 0	$ 0	$ 0

Collaborative Arrangements and Licensing Agreements, Alnylam Pharmaceuticals, Inc. (Details) $ in Thousands	1 Months Ended	3 Months Ended								12 Months Ended
	Mar. 31, 2004 USD ($)	Dec. 31, 2017 USD ($)	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($) Program Target
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned		$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Alnylam Pharmaceuticals, Inc. [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront payment recorded as deferred revenue	$ 5,000
Maximum amount of payments receivable per drug for milestone payments		3,400								3,400
Maximum amount of payments receivable per drug for development milestones		1,100								1,100
Maximum amount of payments receivable per drug for regulatory milestones		2,300								2,300
Next prospective milestone		800								800
Maximum amount of payments payable for development and regulatory milestones		3,400								3,400
Number of therapeutic programs \| Program												4
Number of therapeutic targets granted to Ionis \| Target												4
Number of other unnamed therapeutic targets granted to Ionis \| Target												2
Number of therapeutic targets granted by Ionis \| Target												4
Cumulative payments received		$ 70,000								70,000
Revenue earned										$ 3,300	$ 1,100	$ 1,300

Collaborative Arrangements and Licensing Agreements, Antisense Therapeutics Limited (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Antisense Therapeutics Limited [Member] \| Maximum [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Ownership interest percentage	10.00%				10.00%				10.00%	10.00%
Antisense Therapeutics Limited [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned									$ 0	$ 0	$ 0

Collaborative Arrangements and Licensing Agreements, Atlantic Pharmaceuticals Limited (Details) - USD ($)
$ in Thousands

1 Months Ended

3 Months Ended

12 Months Ended

Mar. 31, 2007

Dec. 31, 2017

Sep. 30, 2017

Jun. 30, 2017

Mar. 31, 2017

Dec. 31, 2016

Sep. 30, 2016

Jun. 30, 2016

Mar. 31, 2016

Dec. 31, 2017

Dec. 31, 2016

Dec. 31, 2015

Atlantic Pharmaceuticals Limited [Member]

$ 172,299

$ 120,911

$ 104,152

$ 110,304

$ 160,349

$ 110,927

$ 38,470

$ 36,874

$ 507,666

$ 346,620

$ 283,703

Collaborative Arrangement and Licensing Agreement [Abstract]

Ownership interest percentage

9.00%

Atlantic Pharmaceuticals Limited [Member]

Collaborative Arrangement and Licensing Agreement [Abstract]

Upfront fee in the form of equity securities

$ 2,000

Maximum amount of payments receivable for regulatory milestones

$ 1,400

Next prospective milestone

$ 600

600

Collaborative Arrangement and Licensing Agreement [Abstract]

$ 0

^[1]

[1]	Revenue from this relationship was negligible for the year.

Collaborative Arrangements and Licensing Agreements, Dynacure, SAS (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Dynacure, SAS [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Ownership interest percentage	15.00%								15.00%
Maximum amount of payments receivable for license fees and substantive milestones	$ 210,000								$ 210,000
Maximum amount of payments receivable for development milestones	34,500								34,500
Maximum amount of payments receivable for regulatory milestones	111,000								111,000
Maximum amount of payments receivable for commercialization milestones	$ 60,000								60,000
Revenue earned									$ 0	$ 0

Collaborative Arrangements and Licensing Agreements, Regulus Therapeutics Inc. (Details) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2017 USD ($)	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($) Drug	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Regulus Therapeutics Inc. [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Number of drugs currently in development \| Drug									2
Revenue earned									$ 0	0	0
Gain on sale of stock											20,211
Proceeds from sale of stock									$ 2,507	$ 4,467	$ 25,527

Collaborative Arrangements and Licensing Agreements, Suzhou Ribo Life Science Co., Ltd. (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended								12 Months Ended
	Apr. 30, 2017	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Collaborative Arrangement and Licensing Agreement [Abstract]
Revenue earned		$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874	$ 507,666	$ 346,620	$ 283,703
Suzhou Ribo Life Science Co., Ltd. [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Upfront payment recorded as deferred revenue	$ 2,000
Ownership interest percentage		9.00%								9.00%
Maximum amount of payments receivable for license fees and substantive milestones		$ 152,900								$ 152,900
Maximum amount of payments receivable for development milestones		13,300								13,300
Maximum amount of payments receivable for commercialization milestones		138,400								$ 138,400
Royalty percentage received on sales of drug										20.00%
Cumulative payments received		2,000								$ 2,000
Next prospective milestone		3,300								3,300
Revenue earned										700
Deferred revenue		$ 1,700								$ 1,700

Collaborative Arrangements and Licensing Agreements, The University of Texas MD Anderson Cancer Center (Details)	12 Months Ended
	Dec. 31, 2017
The University of Texas MD Anderson Cancer Center [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Term of collaboration agreement	5 years

Collaborative Arrangements and Licensing Agreements, External Project Funding (Details) - USD ($)
$ in Thousands

1 Months Ended

3 Months Ended

12 Months Ended

Aug. 31, 2016

Dec. 31, 2017

Sep. 30, 2017

Jun. 30, 2017

Mar. 31, 2017

Dec. 31, 2016

Sep. 30, 2016

Jun. 30, 2016

Mar. 31, 2016

Dec. 31, 2017

Dec. 31, 2016

Dec. 31, 2015

CHDI Foundation, Inc. [Member]

$ 172,299

$ 120,911

$ 104,152

$ 110,304

$ 160,349

$ 110,927

$ 38,470

$ 36,874

$ 507,666

$ 346,620

$ 283,703

Collaborative Arrangement and Licensing Agreement [Abstract]

Cumulative payments made

19,300

Cystic Fibrosis Foundation [Member]

$ 0

^[1]

Collaborative Arrangement and Licensing Agreement [Abstract]

Upfront payment recorded as deferred revenue

$ 1,000

Maximum amount of payments receivable

2,000

Maximum costs specific to collaboration to be shared evenly with partner

3,000

Maximum amount of payments payable for regulatory and commercialization milestones

18,000

Next prospective milestone

800

Cumulative payments received

$ 2,700

2,700

Milestone payments received

1,000

Quarterly Financial Data (Unaudited) [Abstract]

$ 1,900

$ 600

[1]	Revenue from this relationship was negligible for the year.

Collaborative Arrangements and Licensing Agreements, In-Licensing Agreements (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016
Collaborative Arrangement and Licensing Agreement [Abstract]
Accrued liability	$ 66,618	$ 36,013
University of Massachusetts [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Payments for license fees, milestone payments received and royalty on sales of SPINRAZA	9,700	400
Accrued liability	12,900
Cold Spring Harbor Laboratory [Member]
Collaborative Arrangement and Licensing Agreement [Abstract]
Payments for license fees, milestone payments received and royalty on sales of SPINRAZA	$ 13,100	$ 3,400

Segment Information and Concentration of Business Risk, Segment Information (Details) $ in Thousands	3 Months Ended								5 Months Ended	7 Months Ended	12 Months Ended
	Dec. 31, 2017 USD ($)	Sep. 30, 2017 USD ($)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2017 USD ($)	Jul. 18, 2017	Dec. 31, 2017 USD ($) Segment	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Segment Information [Abstract]
Number of reportable segments \| Segment											2
Percentage ownership before IPO										100.00%
Percentage of results included in consolidation										100.00%
Percentage ownership after IPO									68.00%
Commercial Revenue [Abstract]
SPINRAZA royalties											$ 112,540	$ 883	$ 0
Licensing and other royalty revenue											9,519	19,839	2,343
Total commercial revenue											122,059	20,722	2,343
R&D revenue under collaborative agreements											385,607	325,898	281,360
Total segment revenue	$ 172,299	$ 120,911	$ 104,152	$ 110,304	$ 160,349	$ 110,927	$ 38,470	$ 36,874			507,666	346,620	283,703
Total operating expenses	173,992	107,002	105,823	96,315	119,194	94,819	87,397	91,526			483,132	392,936	359,465
Income (loss) from operations	(1,693)	$ 13,909	$ (1,671)	$ 13,989	41,155	$ 16,108	$ (48,927)	$ (54,652)			24,534	(46,316)	(75,762)
Total assets	1,322,024				912,467				$ 1,322,024		1,322,024	912,467
Operating Segments [Member] \| Ionis Core [Member]
Commercial Revenue [Abstract]
SPINRAZA royalties											112,540	883
Licensing and other royalty revenue											9,519	19,839	2,343
Total commercial revenue											122,059	20,722
R&D revenue under collaborative agreements											384,805	338,546	284,015
Total segment revenue											506,864	359,268	286,358
Total operating expenses											373,788	322,192	309,492
Income (loss) from operations											133,076	37,076	(23,134)
Total assets	1,341,828				1,067,770				1,341,828		1,341,828	1,067,770
Operating Segments [Member] \| Akcea Therapeutics [Member]
Commercial Revenue [Abstract]
SPINRAZA royalties											0	0
Licensing and other royalty revenue											0	0	0
Total commercial revenue											0	0
R&D revenue under collaborative agreements											55,209	0	0
Total segment revenue											55,209	0	0
Total operating expenses											163,871	83,512	52,748
Income (loss) from operations											(108,662)	(83,512)	(52,748)
Total assets	268,804				10,684				268,804		268,804	10,684
Elimination of Intercompany Activity [Member]
Commercial Revenue [Abstract]
SPINRAZA royalties											0	0
Licensing and other royalty revenue											0	0	0
Total commercial revenue											0	0
R&D revenue under collaborative agreements											(54,407)	(12,648)	(2,655)
Total segment revenue											(54,407)	(12,648)	(2,655)
Total operating expenses											(54,527)	(12,768)	(2,775)
Income (loss) from operations											120	120	$ 120
Total assets	$ (288,608)				$ (165,987)				$ (288,608)		$ (288,608)	$ (165,987)

Segment Information and Concentration of Business Risk, Revenue from Significant Partners (Details) - Partner	12 Months Ended
	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Revenue [Member] \| Customer Concentration [Member] \| Partner A [Member]
Significant Partners [Abstract]
Concentration percentage	51.00%	60.00%	37.00%
Revenue [Member] \| Customer Concentration [Member] \| Partner B [Member]
Significant Partners [Abstract]
Concentration percentage	14.00%	2.00%	33.00%
Revenue [Member] \| Customer Concentration [Member] \| Partner C [Member]
Significant Partners [Abstract]
Concentration percentage	10.00%	2.00%	11.00%
Revenue [Member] \| Customer Concentration [Member] \| Partner D [Member]
Significant Partners [Abstract]
Concentration percentage	11.00%	0.00%	0.00%
Revenue [Member] \| Customer Concentration [Member] \| Partner E [Member]
Significant Partners [Abstract]
Concentration percentage	3.00%	19.00%	2.00%
Revenue [Member] \| Customer Concentration [Member] \| Partner F [Member]
Significant Partners [Abstract]
Concentration percentage	2.00%	4.00%	12.00%
Contracts Receivables [Member] \| Credit Concentration [Member] \| Significant Partners [Member]
Significant Partners [Abstract]
Concentration percentage	84.00%	92.00%
Number of significant partners	2	2

Employment Benefits (Details) - USD ($)	12 Months Ended
Employment Benefits (Details) - USD ($)	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Employment Benefits [Abstract]
Employee contribution limit per calendar year for employees under 50 years of age	$ 18,000
Employee contribution limit per calendar year for employees over 50 years of age	24,000
Matching contributions	$ 3,000,000	$ 1,700,000	$ 1,500,000

Legal Proceedings (Details) - Suit Related to U.S. Patent Nos. 7,105,499 and 8,481,712 [Member] $ in Billions	1 Months Ended
	Mar. 31, 2016 USD ($) Claim Defense
Legal Proceedings [Abstract]
Number of asserted claims \| Claim	10
Percentage of entitled past sales of sofosbuvir included in award	4.00%
Past sales of sofosbuvir included in award \| $	$ 5
Number of additional non-jury defenses asserted \| Defense	2

Quarterly Financial Data (Unaudited) (Details) - USD ($)
$ / shares in Units, shares in Thousands, $ in Thousands

3 Months Ended

12 Months Ended

Dec. 31, 2017

Sep. 30, 2017

Jun. 30, 2017

Mar. 31, 2017

Dec. 31, 2016

Sep. 30, 2016

Jun. 30, 2016

Mar. 31, 2016

Dec. 31, 2017

Dec. 31, 2016

Dec. 31, 2015

Revenue

$ 172,299

$ 120,911

$ 104,152

$ 110,304

$ 160,349

$ 110,927

$ 38,470

$ 36,874

$ 507,666

$ 346,620

$ 283,703

Operating expenses

173,992

107,002

105,823

96,315

119,194

94,819

87,397

91,526

483,132

392,936

359,465

Income (loss) from operations

(1,693)

13,909

(1,671)

13,989

41,155

16,108

(48,927)

(54,652)

24,534

(46,316)

(75,762)

Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders

(4,662)

(4,896)

(11,206)

3,468

$ 25,865

$ 7,351

$ (56,855)

$ (62,917)

(17,296)

(86,556)

(88,278)

$ 2,744

$ (976)

$ (11,206)

$ 3,468

$ (5,970)

$ (86,556)

$ (88,278)

Basic net income (loss) per share (in dollars per share)

$ 0.02

^[1],[2]

$ 0.00

^[1],[2]

$ (0.09)

^[2]

$ 0.03

^[2]

$ 0.21

^[2]

$ 0.06

^[2]

$ (0.47)

^[2]

$ (0.52)

^[2]

$ 0.08

$ (0.72)

$ (0.74)

Diluted net income (loss) per share (in dollars per share)

$ 0.02

^[2]

$ 0.00

^[2]

$ (0.09)

^[2]

$ 0.03

^[2],[3]

$ 0.21

^[2],[4]

$ 0.06

^[2],[5]

$ (0.47)

^[2]

$ (0.52)

^[2]

$ 0.08

$ (0.72)

$ (0.74)

Income (Numerator) [Abstract]

Income (loss) available to Ionis common stockholders

$ 2,717

$ (419)

$ 3,468

$ 25,865

$ 7,351

$ 9,661

Income available to Ionis common shareholders, plus assumed conversions

$ 2,717

$ 3,468

$ 25,865

$ 7,351

$ 9,661

Shares (Denominator) [Abstract]

Shares used in computing basic net income (loss) per share (in shares)

124,818

124,370

122,861

121,340

120,989

124,016

120,933

119,719

Effect of Diluted Securities [Abstract]

Shares issuable related to our ESPP (in shares)

Shares used in computing diluted net income per share (in shares)

126,862

124,972

123,953

123,378

126,098

120,933

119,719

1 Percent Convertible Senior Notes [Member]

Convertible Senior Notes [Abstract]

2 3/4 Percent Convertible Senior Notes [Member]

1.00%

Convertible Senior Notes [Abstract]

Effect of Diluted Securities [Abstract]

2.75%

Stock Options [Member]

Shares issuable related to stock-based compensation (in shares)

1,532

1,674

2,189

2,129

1,619

Restricted Stock Awards [Member]

Effect of Diluted Securities [Abstract]

Shares issuable related to stock-based compensation (in shares)

507

377

403

202

459

Ionis [Member]

Quarterly Financial Data (Unaudited) [Abstract]

Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders

$ 18,672

$ 9,168

$ 92,336

Akcea [Member]

Quarterly Financial Data (Unaudited) [Abstract]

Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders

(15,955)

(9,587)

(82,676)

Akcea [Member] | Common Stock [Member]

Quarterly Financial Data (Unaudited) [Abstract]

Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders

$ (15,955)

$ (9,870)

$ (58,332)

Basic net income (loss) per share (in dollars per share)

$ (0.35)

$ (0.27)

$ (2.82)

Akcea [Member] | Series A Convertible Preferred Stock [Member]

45,448

36,556

20,669

Quarterly Financial Data (Unaudited) [Abstract]

Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders

$ 283

$ (24,344)

Basic net income (loss) per share (in dollars per share)

$ 0.05

$ (1.55)

Dividend rate

6.00%

Conversion ratio

converted into common stock on a 1:1 basis