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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,
 RrZuAzZZhCAADSEjg8FulKoBzo2AvRR5YaCpVHFK2MHXmUdXcZjTnWWs4S3Go5Ze
 xUesykJ5Db7q+PW4ArMKXg==

<SEC-DOCUMENT>0001179110-04-012874.txt : 20040615
<SEC-HEADER>0001179110-04-012874.hdr.sgml : 20040615
<ACCEPTANCE-DATETIME>20040615155453
ACCESSION NUMBER:		0001179110-04-012874
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20040610
FILED AS OF DATE:		20040615

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			YOUNG JOHN A
		CENTRAL INDEX KEY:			0001194929

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-28218
		FILM NUMBER:		04864266

	BUSINESS ADDRESS:	
		STREET 1:		67 S SAN ANTONIO ROAD SUITE 7
		CITY:			LOS ALTOS
		STATE:			CA
		ZIP:			94022-3055
		BUSINESS PHONE:		908 582 3329

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>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-06-10</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001194929</rptOwnerCik>
            <rptOwnerName>YOUNG JOHN 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>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Options to Purchase Common Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>27.19</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-06-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-06-10</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-06-12</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>10000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Granted pursuant to the provisions set forth in the Amended and Restated 1996 Nonemployee Directors Stock Option Plan of Affymetrix, Inc.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ John A. Young</signatureName>
        <signatureDate>2004-06-15</signatureDate>
    </ownerSignature>
</ownershipDocument>

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