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

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2010-08-03</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001076481</issuerCik>
        <issuerName>SEQUENOM INC</issuerName>
        <issuerTradingSymbol>SQNM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001498278</rptOwnerCik>
            <rptOwnerName>VAN DEN BOOM DIRK</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3595 JOHN HOPKINS COURT</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Director, Mol Biology</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>24864</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.34</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-04-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5380</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.09</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-04-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>375</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.38</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-10-19</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3130</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.93</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-07-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>22650</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.4</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-04-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2666</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.92</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-04-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1666</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.66</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-02-11</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>13000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>14.07</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F8"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-11-30</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12082</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>19.14</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F9"/>
            </exerciseDate>
            <expirationDate>
                <value>2012-04-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>25.15</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F10"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-01-15</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1604</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>40.88</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F11"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-02-20</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3333</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Non-Qualified Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.38</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F12"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-10-19</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>26870</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Non-Qualified Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>14.07</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F13"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-11-30</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>7918</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Non-Qualified Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>25.15</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F14"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-01-15</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>9396</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares subject to the option vested in 48 equal monthly installments commencing 4/10/06, such that the shares subject to the option were fully vested on 4/10/10.</footnote>
        <footnote id="F2">The shares subject to the option vested in 48 equal monthly installments commencing 4/1/05, such that the shares subject to the option were fully vested on 4/1/09.</footnote>
        <footnote id="F3">25% of the shares subject to the options vested on 5/1/10, with the remainder vesting in 36 equal monthly installments until fully vested on 5/1/13.</footnote>
        <footnote id="F4">The shares subject to the option vested in 48 equal monthly installments commencing 7/10/07, such that the shares subject to the option were fully vested on 7/10/11.</footnote>
        <footnote id="F5">The shares subject to the option vested in 48 equal monthly installments commencing 4/1/03, such that the shares subject to the option were fully vested on 4/1/07.</footnote>
        <footnote id="F6">The shares subject to the option vested in 48 equal monthly installments commencing 4/1/04, such that the shares subject to the option were fully vested on 4/1/08.</footnote>
        <footnote id="F7">The shares subject to the option vested in 48 equal monthly installments commencing 2/12/08, such that the shares subject to the option will be fully vested on 2/12/12.</footnote>
        <footnote id="F8">The shares subject to the option vested in 48 equal monthly installments commencing 12/1/08, such that the shares subject to the option will be fully vested on 12/1/12.</footnote>
        <footnote id="F9">The shares subject to the option vested in 48 equal monthly installments commencing 4/1/02, such that the shares subject to the option were fully vested on 4/1/06.</footnote>
        <footnote id="F10">The shares subject to the option vested in 48 equal monthly installments commencing 1/16/09, such that the shares subject to the option will be fully vested on 1/16/13.</footnote>
        <footnote id="F11">The shares subject to the option vested in 48 equal monthly installments commencing 2/19/01, such that the shares subject to the option were fully vested on 2/19/05.</footnote>
        <footnote id="F12">25% of the shares subject to the options vested on 5/1/10, with the remainder vesting in 36 equal monthly installments until fully vested on 5/1/13.</footnote>
        <footnote id="F13">The shares subject to the option vested in 48 equal monthly installments commencing 12/1/08, such that the shares subject to the option will be fully vested on 12/1/12.</footnote>
        <footnote id="F14">The shares subject to the option vested in 48 equal monthly installments commencing 1/16/09, such that the shares subject to the option will be fully vested on 1/16/13.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>By: Clarke Neumann, as attorney-in-fact  For: Dirk Van Den Boom</signatureName>
        <signatureDate>2010-08-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
