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  <xs:element name="AstraZenecaCollaborationCardiovascularRenalAndMetabolicDiseasesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_AstraZenecaCollaborationCardiovascularRenalAndMetabolicDiseasesMember"/>
  <xs:element name="AstraZenecaCollaborationWAINUAMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_AstraZenecaCollaborationWAINUAMember"/>
  <xs:element name="AstraZenecaCollaborationWainuaMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_AstraZenecaCollaborationWainuaMember"/>
  <xs:element name="AstraZenecaCollaborationsMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_AstraZenecaCollaborationsMember"/>
  <xs:element name="CollaborativeAgreementRevenueMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_CollaborativeAgreementRevenueMember"/>
  <xs:element name="CommercialMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_CommercialMember"/>
  <xs:element name="ConvertibleSeniorNotes0125PercentMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ConvertibleSeniorNotes0125PercentMember"/>
  <xs:element name="ConvertibleSeniorNotes0PercentMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ConvertibleSeniorNotes0PercentMember"/>
  <xs:element name="ConvertibleSeniorNotes175PercentMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ConvertibleSeniorNotes175PercentMember"/>
  <xs:element name="ConvertibleSeniorNotes1PercentMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ConvertibleSeniorNotes1PercentMember"/>
  <xs:element name="EquitySecuritiesPrivateCompaniesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_EquitySecuritiesPrivateCompaniesMember"/>
  <xs:element name="EquitySecuritiesPubliclyTradedCompaniesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_EquitySecuritiesPubliclyTradedCompaniesMember"/>
  <xs:element name="GrantedIn2024Member" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_GrantedIn2024Member"/>
  <xs:element name="GrantedIn2025Member" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_GrantedIn2025Member"/>
  <xs:element name="IonisOperationsMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_IonisOperationsMember"/>
  <xs:element name="LicenseOfSapablursenMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_LicenseOfSapablursenMember"/>
  <xs:element name="OnoCollaborationMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_OnoCollaborationMember"/>
  <xs:element name="OtherCommercialMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_OtherCommercialMember"/>
  <xs:element name="OtherMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_OtherMember"/>
  <xs:element name="OtherRoyaltiesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_OtherRoyaltiesMember"/>
  <xs:element name="PelacarsenMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_PelacarsenMember"/>
  <xs:element name="ResearchAndDevelopmentRevenueMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ResearchAndDevelopmentRevenueMember"/>
  <xs:element name="ResearchAndDevelopmentServicesForSapablursenMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ResearchAndDevelopmentServicesForSapablursenMember"/>
  <xs:element name="ResearchDevelopmentAndPatentExpensesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_ResearchDevelopmentAndPatentExpensesMember"/>
  <xs:element name="RoyaltyPurchaseAgreementMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_RoyaltyPurchaseAgreementMember"/>
  <xs:element name="SpinrazaMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_SpinrazaMember"/>
  <xs:element name="SpinrazaRoyaltiesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_SpinrazaRoyaltiesMember"/>
  <xs:element name="TegsediAndWaylivraMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_TegsediAndWaylivraMember"/>
  <xs:element name="TryngolzaMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_TryngolzaMember"/>
  <xs:element name="WainuaJointDevelopmentRevenueMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_WainuaJointDevelopmentRevenueMember"/>
  <xs:element name="WainusRoyaltiesMember" type="dtr:domainItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_WainusRoyaltiesMember"/>
  <xs:element name="CollaborativeArrangementsAndLicensingAgreementsAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_CollaborativeArrangementsAndLicensingAgreementsAbstract"/>
  <xs:element name="ConvertibleNotesDisclosureTable" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrldt:hypercubeItem" id="ions_ConvertibleNotesDisclosureTable"/>
  <xs:element name="SupplementalFinancialDataAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_SupplementalFinancialDataAbstract"/>
  <xs:element name="DocumentAndEntityInformationAbstract" type="xbrli:stringItemType" abstract="true" xbrli:periodType="duration" nillable="true" substitutionGroup="xbrli:item" id="ions_DocumentAndEntityInformationAbstract"/>
</xs:schema>
