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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 AaT4nhI9eJNuQ01mEPjmdw==

<SEC-DOCUMENT>0000932440-08-000581.txt : 20080911
<SEC-HEADER>0000932440-08-000581.hdr.sgml : 20080911
<ACCEPTANCE-DATETIME>20080911111650
ACCESSION NUMBER:		0000932440-08-000581
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20080910
FILED AS OF DATE:		20080911
DATE AS OF CHANGE:		20080911

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			SEQUENOM INC
		CENTRAL INDEX KEY:			0001076481
		STANDARD INDUSTRIAL CLASSIFICATION:	MEASURING & CONTROLLING DEVICES, NEC [3829]
		IRS NUMBER:				770365889
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		3595 JOHN HOPKINS CT
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		8582029000

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Ridgeback Capital Management LLC
		CENTRAL INDEX KEY:			0001357610
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-29101
		FILM NUMBER:		081066564

	BUSINESS ADDRESS:	
		STREET 1:		430 PARK AVENUE, 12TH FLOOR
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10022
		BUSINESS PHONE:		212-756-1562

	MAIL ADDRESS:	
		STREET 1:		430 PARK AVENUE, 12TH FLOOR
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10022

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Ridgeback Capital Investments Ltd.
		CENTRAL INDEX KEY:			0001358916
		STATE OF INCORPORATION:			E9
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-29101
		FILM NUMBER:		081066565

	BUSINESS ADDRESS:	
		STREET 1:		430 PARK AVENUE
		STREET 2:		12TH FLOOR
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10022
		BUSINESS PHONE:		212-624-2567

	MAIL ADDRESS:	
		STREET 1:		430 PARK AVENUE
		STREET 2:		12TH FLOOR
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10022

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Ridgeback Capital Investments L.P.
		CENTRAL INDEX KEY:			0001423994
		STATE OF INCORPORATION:			E9
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-29101
		FILM NUMBER:		081066566

	BUSINESS ADDRESS:	
		STREET 1:		430 PARK AVENUE
		STREET 2:		12TH FLOOR
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10022
		BUSINESS PHONE:		212-624-2567

	MAIL ADDRESS:	
		STREET 1:		430 PARK AVENUE
		STREET 2:		12TH FLOOR
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10022
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-09-10</periodOfReport>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001423994</rptOwnerCik>
            <rptOwnerName>Ridgeback Capital Investments L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>430 PARK AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>12TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001358916</rptOwnerCik>
            <rptOwnerName>Ridgeback Capital Investments Ltd.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>430 PARK AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>12TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YOR,</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001357610</rptOwnerCik>
            <rptOwnerName>Ridgeback Capital Management LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>430 PARK AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>12TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-09-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>240000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>19.43</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10495462</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-09-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>85000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>19.60</value>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10580462</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Ridgeback Capital Investments L.P. owns all of securities reported herein directly.  Ridgeback Capital Investments Ltd. is the general partner of Ridgeback Capital Investments L.P.  Pursuant to an investment management agreement, Ridgeback Capital Management LLC maintains investment and voting power with respect to the securities held or controlled by Ridgeback Capital Investments Ltd.  Wayne Holman, an individual, controls Ridgeback Capital Management LLC.  Ridgeback Capital Management LLC, Ridgeback Capital Investments Ltd. and Wayne Holman do not own any securities reported herein directly and disclaim beneficial ownership of any of the securities covered by this statement, except to the extent of any pecuniary interest therein.</footnote>
        <footnote id="F2">Constitutes the weighted average purchase price for multiple transactions reported on this line having prices per share ranging from $19.04 to $19.80.  The Reporting Persons will provide upon request by the Commission staff, the issuer or a security holder of the issuer, full information regarding each separate transaction.</footnote>
        <footnote id="F3">Constitutes the weighted average purchase price for multiple transactions reported on this line having prices per share ranging from $19.24 to $19.85.  The Reporting Persons will provide upon request by the Commission staff, the issuer or a security holder of the issuer, full information regarding each separate transaction.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Bud Holman as Attorney-in-Fact</signatureName>
        <signatureDate>2008-09-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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