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| <?xml version="1.0" encoding="windows-1252"?> |
| <ownershipDocument> |
| <schemaVersion> X0306 </schemaVersion> |
| <documentType> 4 </documentType> |
| <periodOfReport> 2020-02-29 </periodOfReport> |
| <issuer> |
| | <issuerCik> 0000874015 </issuerCik> |
| | <issuerName> IONIS PHARMACEUTICALS INC </issuerName> |
| | <issuerTradingSymbol> IONS </issuerTradingSymbol> |
| | </issuer> |
| <reportingOwner> |
| | <reportingOwnerId> |
| | | <rptOwnerCik> 0001074773 </rptOwnerCik> |
| | | <rptOwnerName> HOUGEN ELIZABETH L </rptOwnerName> |
| | | </reportingOwnerId> |
| | <reportingOwnerAddress> |
| | | <rptOwnerStreet1> 2855 GAZELLE CT. </rptOwnerStreet1> |
| | | <rptOwnerStreet2></rptOwnerStreet2> |
| | | <rptOwnerCity> CARLSBAD </rptOwnerCity> |
| | | <rptOwnerState> CA </rptOwnerState> |
| | | <rptOwnerZipCode> 92010 </rptOwnerZipCode> |
| | | <rptOwnerStateDescription></rptOwnerStateDescription> |
| | | </reportingOwnerAddress> |
| | <reportingOwnerRelationship> |
| | | <isDirector> 0 </isDirector> |
| | | <isOfficer> 1 </isOfficer> |
| | | <isTenPercentOwner> 0 </isTenPercentOwner> |
| | | <isOther> 0 </isOther> |
| | | <officerTitle> SVP, Finance & CFO </officerTitle> |
| | | </reportingOwnerRelationship> |
| | </reportingOwner> |
| <nonDerivativeTable> |
| | <nonDerivativeTransaction> |
| | | <securityTitle> |
| <value> Common Stock </value> |
| </securityTitle> |
| | | <transactionDate> |
| <value> 2020-02-29 </value> |
| </transactionDate> |
| | | <transactionCoding> |
| <transactionFormType> 4 </transactionFormType> |
| <transactionCode> J </transactionCode> |
| <equitySwapInvolved> 0 </equitySwapInvolved> |
| <footnoteId id="F1"/> |
| </transactionCoding> |
| | | <transactionAmounts> |
| <transactionShares> |
| <value> 147 </value> |
| </transactionShares> |
| <transactionPricePerShare> |
| <value> 43.163 </value> |
| </transactionPricePerShare> |
| <transactionAcquiredDisposedCode> |
| <value> A </value> |
| </transactionAcquiredDisposedCode> |
| </transactionAmounts> |
| | | <postTransactionAmounts> |
| <sharesOwnedFollowingTransaction> |
| <value> 32374 </value> |
| </sharesOwnedFollowingTransaction> |
| </postTransactionAmounts> |
| | | <ownershipNature> |
| <directOrIndirectOwnership> |
| <value> D </value> |
| </directOrIndirectOwnership> |
| <natureOfOwnership> |
| <value></value> |
| </natureOfOwnership> |
| </ownershipNature> |
| | | </nonDerivativeTransaction> |
| | </nonDerivativeTable> |
| <footnotes> |
| | <footnote id="F1"> Reporting 147 shares acquired under the Ionis Pharmeceuticals, Inc. Amended and Restated 2000 Employee Stock Purchase Plan on February 29, 2020. These 147 shares may not be sold until August 30, 2020. </footnote> |
| | </footnotes> |
| <remarks></remarks> |
| <ownerSignature> |
| | <signatureName> /s/Patrick R. O'Neil, attorney-in-fact </signatureName> |
| | <signatureDate> 2020-03-03 </signatureDate> |
| | </ownerSignature> |
| </ownershipDocument> |
