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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 BvHHMls81EhG9Drb6GEY2IV4rT0bezKafO+UTRvEpey/Pl51Y1UZrup7fWz2du09
 JZflQYG9JpWpJWNuP5OCBQ==

<SEC-DOCUMENT>0001179110-04-000416.txt : 20040106
<SEC-HEADER>0001179110-04-000416.hdr.sgml : 20040106
<ACCEPTANCE-DATETIME>20040106142510
ACCESSION NUMBER:		0001179110-04-000416
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20040102
FILED AS OF DATE:		20040106

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			FODOR STEPHEN P A
		CENTRAL INDEX KEY:			0001240360

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-28218
		FILM NUMBER:		04509428

	MAIL ADDRESS:	
		STREET 1:		C/O AFFYMETRIX INC
		STREET 2:		3380 CENTRAL EXPRESSWAY
		CITY:			SANTA CLARA
		STATE:			CA
		ZIP:			95051

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>2004-01-02</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
</issuer>
<reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001240360</rptOwnerCik>
            <rptOwnerName>FODOR STEPHEN P A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O AFFYMETRIX, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3380 CENTRAL EXPRESSWAY</rptOwnerStreet2>
            <rptOwnerCity>SANTA CLARA</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>95051</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector>
<isOfficer>1</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle>Chairman and CEO</officerTitle>
<otherText></otherText>
</reportingOwnerRelationship>
</reportingOwner>
<nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2004-01-02</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>10000</value>
</transactionShares>
<transactionPricePerShare><value>.3375</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>A</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>2004-01-02</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>10000</value>
<footnoteId id="F1"></footnoteId>
</transactionShares>
<transactionPricePerShare><value>23.92</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>62270</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
</nonDerivativeTable>
<derivativeTable><derivativeTransaction><securityTitle><value>Options to Purchase Common Stock</value>
</securityTitle>
<conversionOrExercisePrice><value>.3375</value>
</conversionOrExercisePrice>
<transactionDate><value>2004-01-02</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>10000</value>
</transactionShares>
<transactionPricePerShare><value>0</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<exerciseDate><value>1999-12-06</value>
</exerciseDate>
<expirationDate><value>2004-12-06</value>
</expirationDate>
<underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value>
</underlyingSecurityTitle>
<underlyingSecurityShares><value>10000</value>
</underlyingSecurityShares>
</underlyingSecurity>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>76896</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</derivativeTransaction>
</derivativeTable>
<footnotes><footnote id="F1">Sold pursuant to a 10b5-1 Sales Plan entered into on August 6, 2003 by the reporting person.</footnote>
</footnotes>
<ownerSignature><signatureName>/s/ Stephen P.A. Fodor</signatureName>
<signatureDate>2004-01-06</signatureDate>
</ownerSignature>
</ownershipDocument>

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