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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 OgqOZdLeK0f8REVIUMy/5l8D0x/APklVDIb1Z5veC4zZ/hx30TWQDEy6pnbqTPmu
 m9ei8oeAtbxOsKU0q8sBag==

<SEC-DOCUMENT>0001332432-06-000004.txt : 20060118
<SEC-HEADER>0001332432-06-000004.hdr.sgml : 20060118
<ACCEPTANCE-DATETIME>20060118152503
ACCESSION NUMBER:		0001332432-06-000004
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060113
FILED AS OF DATE:		20060118
DATE AS OF CHANGE:		20060118

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Lloyd-Harris Genghis
		CENTRAL INDEX KEY:			0001320486

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		06535488

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		020-7534-1500

	MAIL ADDRESS:	
		STREET 1:		38 JERMYN STREET
		CITY:			LONDON
		STATE:			X0
		ZIP:			SW1Y 6DN

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>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-01-13</periodOfReport>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001320486</rptOwnerCik>
            <rptOwnerName>Lloyd-Harris Genghis</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ABINGWORTH MANAGEMENT LIMITED</rptOwnerStreet1>
            <rptOwnerStreet2>38 JERMYN STREET</rptOwnerStreet2>
            <rptOwnerCity>LONDON</rptOwnerCity>
            <rptOwnerState>X0</rptOwnerState>
            <rptOwnerZipCode>SW1Y 6DN</rptOwnerZipCode>
            <rptOwnerStateDescription>UNITED KINGDOM</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common STock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-01-13</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>3150</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.74</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3150</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The shares were issued pursuant to the Company's 2005 Equity Incentive Plan for payment of retainer and meeting attendance fees.  The shares are fully vested upon issuance and are restricted from sale for twelve months from the date of issuance.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Genghis Lloyd-Harris</signatureName>
        <signatureDate>2006-01-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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