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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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 vuVbO7NZ3Eoav4p24RCNyQ==

<SEC-DOCUMENT>0001332432-05-000033.txt : 20051230
<SEC-HEADER>0001332432-05-000033.hdr.sgml : 20051230
<ACCEPTANCE-DATETIME>20051230150014
ACCESSION NUMBER:		0001332432-05-000033
CONFORMED SUBMISSION TYPE:	3/A
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20050712
FILED AS OF DATE:		20051230
DATE AS OF CHANGE:		20051230

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			West John
		CENTRAL INDEX KEY:			0001320337

	FILING VALUES:
		FORM TYPE:		3/A
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		051294334

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		510-670-9300

	MAIL ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			Solexa, Inc.
		CENTRAL INDEX KEY:			0000913275
		STANDARD INDUSTRIAL CLASSIFICATION:	MEDICINAL CHEMICALS & BOTANICAL PRODUCTS [2833]
		IRS NUMBER:				943161073
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545
		BUSINESS PHONE:		5106709300

	MAIL ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	LYNX THERAPEUTICS INC
		DATE OF NAME CHANGE:	19931008
</SEC-HEADER>
<DOCUMENT>
<TYPE>3/A
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2005-07-12</periodOfReport>

    <dateOfOriginalSubmission>2005-03-14</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000913275</issuerCik>
        <issuerName>Solexa, Inc.</issuerName>
        <issuerTradingSymbol>SLXA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001320337</rptOwnerCik>
            <rptOwnerName>West John</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SOLEXA, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>25861 INDUSTRIAL BLVD.</rptOwnerStreet2>
            <rptOwnerCity>HAYWARD</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94545</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Executive Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.28</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-08-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>309253</value>
                    <footnoteId id="F2"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Shares will vest monthly from the vesting commencement date, August 6, 2004, over a four year period.</footnote>
        <footnote id="F2">The number of shares subject to the stock option was reduced by 2,462 shares in connection with the reallocation of an aggregate of 7,198 shares of common stock of Solexa, Inc. (the &quot;Company&quot;) to the former shareholders of Solexa Limited in connection with the business combination between the Company and Solexa Limited completed on March 4, 2005.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>John West</signatureName>
        <signatureDate>2005-12-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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