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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2013-05-20</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001577539</rptOwnerCik>
            <rptOwnerName>Wood Gavin</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O AFFYMETRIX, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3420 CENTRAL EXPRESSWAY</rptOwnerStreet2>
            <rptOwnerCity>SANTA CLARA</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>95051</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Financial Officer</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>16412</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>24.66</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-11-29</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>25.71</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-06-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>600</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.29</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-06-23</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.71</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-08-21</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.97</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-02-19</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.29</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-08-20</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Comon Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.22</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F8"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-08-19</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4900</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.31</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F9"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-02-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.85</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F10"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-11-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.16</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F11"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-07-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.91</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F12"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-08-30</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.77</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F13"/>
            </exerciseDate>
            <expirationDate>
                <value>2020-02-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>8000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.77</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F13"/>
            </exerciseDate>
            <expirationDate>
                <value>2020-02-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>22000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Includes the following restricted stock units (&quot;RSUs&quot;), each of which vests in equal anual installments over four years from the grant date, less the number of shares withheld for tax purposes on subsequent scheduled vesting date(s) on or before May 20, 2013 (&quot;Shares Withheld&quot;): (1) 1,225 RSUs granted on August 19, 2010 less 289 Shares Withheld, (2) 1,400 RSUs granted on February 17, 2011 less 294 Shares Withheld, (3) 6,000 RSUs granted on November 17, 2011 less 630 Shares Withheld, (4) 1,500 RSUs granted on July 26, 2012, (5) 1,500 RSUs granted on Augst 30, 2012 and (6) 6,000 RSUs granted on February 7, 2013.</footnote>
        <footnote id="F2">Stock option becomes exercisable in equal annual installments over four years from the grant date of November 29, 2006.</footnote>
        <footnote id="F3">Stock option becomes exercisable in equal annual installments over four years from the grant date of June 6, 2007.</footnote>
        <footnote id="F4">Stock option becomes exercisable in equal annual installments over four years from the grant date of June 23, 2008.</footnote>
        <footnote id="F5">Stock option becomes exercisable in equal annual installments over four years from the grant date of August 21, 2008.</footnote>
        <footnote id="F6">Stock option becomes exercisable in equal annual installments over four years from the grant date of February 19, 2009.</footnote>
        <footnote id="F7">Stock option becomes exercisable in equal annual installments over four years from the grant date of August 20, 2009.</footnote>
        <footnote id="F8">Stock option becomes exercisable in equal annual installments over four years from the grant date of August 19, 2010.</footnote>
        <footnote id="F9">Stock option becomes exercisable in equal annual installments over four years from the grant date of February 17, 2011.</footnote>
        <footnote id="F10">Stock option becomes exercisable in equal annual installments over four years from the grant date of November 17, 2011.</footnote>
        <footnote id="F11">Stock option becomes exercisable in equal annual installments over four years from the grant date of July 26, 2012.</footnote>
        <footnote id="F12">Stock option becomes exercisable in equal annual installments over four years from the grant date of August 30, 2012.</footnote>
        <footnote id="F13">Stock option becomes exercisable in equal annual installments over four years from the grant date of February 7, 2013.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Siang H. Chin, Attorney-in-Fact for Gavin Wood</signatureName>
        <signatureDate>2013-05-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
