-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 Tqp8zaHUvRcLCI7md5I6l15QC35ZdFIzldff9YqjEVz8fqLL8tEHj0B8dvDEz1vS
 QcqoIuAdJDIfcPephPMQsg==

<SEC-DOCUMENT>0001179110-03-010784.txt : 20031114
<SEC-HEADER>0001179110-03-010784.hdr.sgml : 20031114
<ACCEPTANCE-DATETIME>20031114164146
ACCESSION NUMBER:		0001179110-03-010784
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20031112
FILED AS OF DATE:		20031114

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			LOUCKS VERNON R JR
		CENTRAL INDEX KEY:			0001183294

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-28218
		FILM NUMBER:		031005297

	BUSINESS ADDRESS:	
		STREET 1:		THE AETHENA GROUP, LLC
		STREET 2:		1101 SKOKIE BLVD., STE. 240
		CITY:			NORTHBROOK
		STATE:			IL
		ZIP:			60062
		BUSINESS PHONE:		8479483600

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			AFFYMETRIX INC
		CENTRAL INDEX KEY:			0000913077
		STANDARD INDUSTRIAL CLASSIFICATION:	LABORATORY ANALYTICAL INSTRUMENTS [3826]
		IRS NUMBER:				770319159
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		3380 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051
		BUSINESS PHONE:		4085226000

	MAIL ADDRESS:	
		STREET 1:		3380 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>FORM 4 -
<TEXT>
<XML>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2003-11-12</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
</issuer>
<reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001183294</rptOwnerCik>
            <rptOwnerName>LOUCKS VERNON R JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>THE AETHENA GROUP</rptOwnerStreet1>
            <rptOwnerStreet2>1101 SKOKIE BOULEVARD SUITE 240</rptOwnerStreet2>
            <rptOwnerCity>NORTHBROOK</rptOwnerCity>
            <rptOwnerState>IL</rptOwnerState>
            <rptOwnerZipCode>60062</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector>
<isOfficer>0</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle></officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2003-11-12</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>2900</value>
</transactionShares>
<transactionPricePerShare><value>25.14</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
<nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2003-11-12</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>100</value>
</transactionShares>
<transactionPricePerShare><value>25.11</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>73664</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
<nonDerivativeHolding><securityTitle><value>Common Stock</value>
</securityTitle>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>8096</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>I</value>
</directOrIndirectOwnership>
<natureOfOwnership><value>Linda Loucks</value>
<footnoteId id="F1"></footnoteId>
</natureOfOwnership>
</ownershipNature>
</nonDerivativeHolding>
</nonDerivativeTable>
<derivativeTable></derivativeTable>
<footnotes><footnote id="F1">Held by spouse Linda Loucks.</footnote>
</footnotes>
<ownerSignature><signatureName>/s/ Vernon R. Loucks, Jr.</signatureName>
<signatureDate>2003-11-14</signatureDate>
</ownerSignature>
</ownershipDocument>

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