-----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,
 IqOGC6IpY6xdhxCcbKk3PAZV4oe84LLkYEpmVFHmlkiLmDjp4ir/hq/m7OWeThKQ
 k+SunIHVkK9PvzZHkdi0qw==

<SEC-DOCUMENT>0000874015-03-000044.txt : 20030513
<SEC-HEADER>0000874015-03-000044.hdr.sgml : 20030513
<ACCEPTANCE-DATETIME>20030513174356
ACCESSION NUMBER:		0000874015-03-000044
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:			PARSHALL B LYNNE
		CENTRAL INDEX KEY:			0001073385

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-19125
		FILM NUMBER:		03696527

	BUSINESS ADDRESS:	
		STREET 1:		2292 FARADAY AVENUE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
		BUSINESS PHONE:		7606032460

	MAIL ADDRESS:	
		STREET 1:		2292 FARADAY AVENUE
		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>2003-05-09</periodOfReport>
<issuer><issuerCik>0000874015</issuerCik>
        <issuerName>ISIS PHARMACEUTICALS INC</issuerName>
<issuerTradingSymbol>ISIS</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId><rptOwnerCik>0001073385</rptOwnerCik>
            <rptOwnerName>PARSHALL B LYNNE</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
<reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>Executive Vice President, CFO</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>56466</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><expirati
onDate><value>2008-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>56466</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>56466</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>12.625</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></transactionCodin
g><transactionAmounts><transactionShares><value>60000</value><footnoteId id="F2"/></transactionShares><transactionValue><value>12.625</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2000-12-14</value></exerciseDate><expirationDate><value>2005-12-13</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>60000</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>13.125
</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>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><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>18</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>17000</value><footnoteId id="F2"/></transactionShares><transactionValue><value>18</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2001-01-01</value></exerciseDate><expirationDate><value>2006-12-31</value></expirationDate><underlyi
ngSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>17000</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>35000</value><f
ootnoteId 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></underlyingSecurityTitle><underlyingSecurityShares><value>35000</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.  There
after, the remaining shares subject to the option vest and become exercisable in 24 equal monthly installments, at the rate of 18,822 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/B. Lynne Parshall</signatureName><signatureDate>2003-05-13</signatureDate></ownerSignature></ownershipDocument>

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</SEC-DOCUMENT>
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