-----BEGIN PRIVACY-ENHANCED MESSAGE-----
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,
 MJWOT2MvNFOrcZ/gf9AwAdowjNopctSMlR3NEYYlX+1CUjYirXpEstqgPfoF3nD6
 GeM28RZf1D7RQ5mBuibmvg==

<SEC-DOCUMENT>0001332432-06-000019.txt : 20060706
<SEC-HEADER>0001332432-06-000019.hdr.sgml : 20060706
<ACCEPTANCE-DATETIME>20060706124844
ACCESSION NUMBER:		0001332432-06-000019
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060705
FILED AS OF DATE:		20060706
DATE AS OF CHANGE:		20060706

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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Omead Ostadan
		CENTRAL INDEX KEY:			0001368212

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		06947109

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		510-670-9300

	MAIL ADDRESS:	
		STREET 1:		SOLEXA, INC.
		STREET 2:		25861 INDUSTRIAL BLVD.
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-07-05</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001368212</rptOwnerCik>
            <rptOwnerName>Omead Ostadan</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>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Vice President, Marketing</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.11</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-05-31</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-06-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>50000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>8.60</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2006-02-02</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-02-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>75000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Shares vest over four years from the date awarded with 25% vesting on the first anniversary of the date of grant, and the remainder vesting at a rate of 1/36 per complete month thereafter.  Shares are exercisable once vested.</footnote>
        <footnote id="F2">Shares vest over five years from the date awarded with 20% vesting on the first anniversary of the date of grant, and the remainder vesting at a rate of 1/48 per complete month thereafter.  Shares are exercisable once vested.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Omead Ostadan</signatureName>
        <signatureDate>2006-07-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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