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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 EcrdSVDP+Zfb6aJfF66VBlW/1Y0tXHm3n7pS1diEEicgqF+t8J9DVVqgWgHG6qwZ
 PoMgRu62zU3zXHaXepVj/A==

<SEC-DOCUMENT>0000874015-03-000077.txt : 20030716
<SEC-HEADER>0000874015-03-000077.hdr.sgml : 20030716
<ACCEPTANCE-DATETIME>20030716161318
ACCESSION NUMBER:		0000874015-03-000077
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030714
FILED AS OF DATE:		20030716

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			GARIELI CHRISTOPHER
		CENTRAL INDEX KEY:			0001181553
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-19125
		FILM NUMBER:		03789610

	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>2003-07-14</periodOfReport>
    <issuer>
        <issuerCik>0000874015</issuerCik>
        <issuerName>ISIS PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>ISIS</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId>
            <rptOwnerCik>0001181553</rptOwnerCik>
            <rptOwnerName>GARIELI CHRISTOPHER</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><nonDerivativeSecurity><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2003-07-14</value></transactionDate><deemedExecutionDate><value>2003-07-14</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>S</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>10528</value><footnoteId id="F1"/></transactionShares><transactionValue><value>5.5056</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>158951</value><footnoteId id="F2"/><footnoteId id="F3"/><footnoteId id="F4"/></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectO
wnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>See Footnotes 2 and 3</value></natureOfOwnership></ownershipNature></nonDerivativeSecurity><nonDerivativeSecurity><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2003-07-15</value></transactionDate><deemedExecutionDate><value>2003-07-15</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>S</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>20000</value><footnoteId id="F1"/></transactionShares><transactionValue><value>5.45</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>138951</value><footnoteId id="F2"/><footnoteId id="F3"/><footnoteId id="F4"/></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><direc
tOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>See Footnotes 2 and 3</value></natureOfOwnership></ownershipNature></nonDerivativeSecurity><footnotes><footnote id="F1">The shares sold were held by Bessemer Venture Partners III L.P. (&quot;BVP III&quot;).  The reporting person is a General Partner of Deer III &amp; Co., the sole General Partner of BVP III.  The reporting person disclaims beneficial ownership except to the extent of his partnership interest.</footnote><footnote id="F2">Owned by BVP III.  The reporting person is a General Partner of Deer III &amp; Co., the sole General Partner of BVP III.  The reporting person disclaims beneficial ownership except to the extent of his partnership interest.</footnote><footnote id="F3">740 shares owned indirectly by the Gabrieli Family Foundation, a charitable foundation.  The reporting person may be deemed to be a beneficial owner of such shares by viture of his position as Trustee, but disclaims beneficial ownership.</
footnote><footnote id="F4">155,431 shares owned directly</footnote></footnotes><ownerSignature><signatureName>B. Lynne Parshall, by Power of Attorney</signatureName><signatureDate>2003-07-15</signatureDate></ownerSignature></ownershipDocument>

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