-----BEGIN PRIVACY-ENHANCED MESSAGE-----
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,
 QTRq1n0Grm8Il2uDSKcVgTE7sctg7eLO67YjJDeC1owWM5qr55+VdUaX/fxLHmwz
 ZYlpncaO5sfStpUwc9J1rQ==

<SEC-DOCUMENT>0000874015-03-000042.txt : 20030513
<SEC-HEADER>0000874015-03-000042.hdr.sgml : 20030513
<ACCEPTANCE-DATETIME>20030513174201
ACCESSION NUMBER:		0000874015-03-000042
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030509
FILED AS OF DATE:		20030513

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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			LOWENSTAM PATRICIA
		CENTRAL INDEX KEY:			0001073386
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-19125
		FILM NUMBER:		03696519

	BUSINESS ADDRESS:	
		STREET 1:		2292 FARADAY AVE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
		BUSINESS PHONE:		760-6032460

	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>
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<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

<documentType>4</documentType><periodOfReport>2003-05-09</periodOfReport>
<issuer><issuerCik>0000874015</issuerCik>
        <issuerName>ISIS PHARMACEUTICALS INC</issuerName>
<issuerTradingSymbol>ISIS</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId><rptOwnerCik>0001073386</rptOwnerCik>
            <rptOwnerName>LOWENSTAM PATRICIA</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
<reportingOwnerRelationship>
<isDirector>0</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>Vice President</officerTitle></reportingOwnerRelationship></reportingOwner><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>5.15</value></conversionOrExercisePrice><transactionDate><value>2003-05-09</value></transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>39899</value><footnoteId id="F1"/></transactionShares><transactionValue><value>5.15</value></transactionValue><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2004-01-01</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2
008-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>39899</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>39899</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>6.75</value></conversionOrExercisePrice><transactionDate><value>2003-05-09</value></transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmo
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nOrExercisePrice><transactionDate><value>2003-05-09</value></transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>16000</value><footnoteId id="F2"/></transactionShares><transactionValue><value>13.125</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2000-01-01</value></exerciseDate><expirationDate><value>2005-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>16000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><d
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ngSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>8500</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>12.3125</value></conversionOrExercisePrice><transactionDate><value>2003-05-09</value></transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>12000</value><footnoteId id="F2"/>
</transactionShares><transactionValue><value>12.3125</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2002-01-01</value></exerciseDate><expirationDate><value>2007-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>12000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>12.9375</value></conversionOrExercisePrice><transactionDate><value>2003-05-09</value></
transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>15000</value><footnoteId id="F2"/></transactionShares><transactionValue><value>12.9375</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-01-01</value></exerciseDate><expirationDate><value>2008-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>15000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectO
wnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>21.05</value></conversionOrExercisePrice><transactionDate><value>2003-05-09</value></transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>11000</value><footnoteId id="F2"/></transactionShares><transactionValue><value>21.05</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2006-01-02</value></exerciseDate><expirationDate><value>2012-01-01</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyi
ngSecurityTitle><underlyingSecurityShares><value>11000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>21.05</value></conversionOrExercisePrice><transactionDate><value>2003-05-09</value></transactionDate><deemedExecutionDate><value>2003-05-09</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>D</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>10000</value><footnoteId id="F2"/></transactionShares><transactionValue><value>21.05</va
lue></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2006-01-02</value></exerciseDate><expirationDate><value>2012-01-01</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>10000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><footnotes><footnote id="F1">These options were issued in connection with the Company's option exchange program.  33.34% of the shares subject to the option vest and become exercisable on 01/01/2004.  Thereafter, the remaining shares subject to the option vest and become exercis
able in 24 equal monthly installments, at the rate of 13,300 and 13,299, respectively, shares per year.  The option is exercisable as to 0 shares on 05/09/2003.</footnote><footnote id="F2">These options were cancelled in connection with the Company's option exchange program</footnote></footnotes><ownerSignature><signatureName>/s/Patricia Lowenstam</signatureName><signatureDate>2003-05-13</signatureDate></ownerSignature></ownershipDocument>

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</SEC-DOCUMENT>
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