-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 UvhaiEnLdLPDmg3Yop5OlTRw9N6PyZFHk/gYApZ3akY/ZmDDTxgX/joS5Zo7cpRY
 kj6lyXGDqDrV7YDdu64LAA==

<SEC-DOCUMENT>0001179110-03-006613.txt : 20030829
<SEC-HEADER>0001179110-03-006613.hdr.sgml : 20030829
<ACCEPTANCE-DATETIME>20030829160634
ACCESSION NUMBER:		0001179110-03-006613
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030828
FILED AS OF DATE:		20030829

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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			BERG PAUL
		CENTRAL INDEX KEY:			0001198229

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-28218
		FILM NUMBER:		03874382

	BUSINESS ADDRESS:	
		STREET 1:		STANFORD UNIVERSITY SCHOOL OF MEDICINE
		STREET 2:		BECKMAN CENTER #B062
		CITY:			STANFORD
		STATE:			CA
		ZIP:			94305
		BUSINESS PHONE:		6507236170

	MAIL ADDRESS:	
		STREET 1:		STANFORD UNIVERSITY SCHOOL OF MEDICINE
		STREET 2:		#B062
		CITY:			STANFORD
		STATE:			CA
		ZIP:			94305
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>FORM 4 -
<TEXT>
<XML>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2003-08-28</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000913077</issuerCik>
        <issuerName>AFFYMETRIX INC</issuerName>
        <issuerTradingSymbol>AFFX</issuerTradingSymbol>
</issuer>
<reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198229</rptOwnerCik>
            <rptOwnerName>BERG PAUL</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><nonDerivativeTransaction><securityTitle><value>Common Stock</value>
</securityTitle>
<transactionDate><value>2003-08-28</value>
</transactionDate>
<transactionCoding><transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved>
</transactionCoding>
<transactionAmounts><transactionShares><value>2500</value>
</transactionShares>
<transactionPricePerShare><value>23.40</value>
</transactionPricePerShare>
<transactionAcquiredDisposedCode><value>D</value>
</transactionAcquiredDisposedCode>
</transactionAmounts>
<postTransactionAmounts><sharesOwnedFollowingTransaction><value>74836</value>
</sharesOwnedFollowingTransaction>
</postTransactionAmounts>
<ownershipNature><directOrIndirectOwnership><value>D</value>
</directOrIndirectOwnership>
</ownershipNature>
</nonDerivativeTransaction>
</nonDerivativeTable>
<derivativeTable></derivativeTable>
<footnotes></footnotes>
<ownerSignature><signatureName>/s/ Paul Berg</signatureName>
<signatureDate>2003-08-29</signatureDate>
</ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----