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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 RVT7L0DYoa94ETqHPZZsV60QsvRJPeuYuDMoS89eJIkwHGF9yR3Dl3oAjGGrVZaE
 FKutpKgYCvjrp8usPdGa8g==

<SEC-DOCUMENT>0000874015-03-000066.txt : 20030702
<SEC-HEADER>0000874015-03-000066.hdr.sgml : 20030702
<ACCEPTANCE-DATETIME>20030702172022
ACCESSION NUMBER:		0000874015-03-000066
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030701
FILED AS OF DATE:		20030702

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			MUTO FREDERICK T
		CENTRAL INDEX KEY:			0001181560
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-19125
		FILM NUMBER:		03772918

	BUSINESS ADDRESS:	
		STREET 1:		2292 FARADAY AVENUE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
		BUSINESS PHONE:		7609319200

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ISIS PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000874015
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				330336973
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		2292 FARADAY AVE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
		BUSINESS PHONE:		7609319200

	MAIL ADDRESS:	
		STREET 1:		2292 FARADAY AVE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-07-01</periodOfReport>
    <issuer>
        <issuerCik>0000874015</issuerCik>
        <issuerName>ISIS PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>ISIS</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId>
            <rptOwnerCik>0001181560</rptOwnerCik>
            <rptOwnerName>MUTO FREDERICK T</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><derivativeSecurity><securityTitle><value>Director Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>5.17</value></conversionOrExercisePrice><transactionDate><value>2003-07-01</value></transactionDate><deemedExecutionDate><value>2003-07-01</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>10000</value></transactionShares><transactionValue><value>5.17</value></transactionValue><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2004-07-01</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2013-06-30</value></expirationDate><underlyingSecurity><underlyin
gSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>10000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>10000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><footnotes><footnote id="F1">Grant of 7-1-03 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 2002 Non-Employee Directors' Stock Option Plan.  The option vests and becomes exercisable in four equal annual installments, with the first installment vesting on 7-1-04.  The option shall be fully vested and exercisable on 7-1-07.  The option is exercisable as to 0 shares on 7-1-03.</footnote></footnotes><ownerSignature><signatureName>B. Lynne Parshall, by Power of Attorney</signatureName><signatureDate>2003-07-02</signa
tureDate></ownerSignature></ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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