-----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,
 N9PI2LKiSSlUXErOvR8U0RRraSLhJfZMUcMjtKfWFR3UULVbzc8G6XmXKmUo34ul
 qwDGMin/NtmfDbjHyzGVIg==

<SEC-DOCUMENT>0001012975-06-000014.txt : 20060118
<SEC-HEADER>0001012975-06-000014.hdr.sgml : 20060118
<ACCEPTANCE-DATETIME>20060118191148
ACCESSION NUMBER:		0001012975-06-000014
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:			CARTHY MARK
		CENTRAL INDEX KEY:			0001286397

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		06536571

	MAIL ADDRESS:	
		STREET 1:		222 BERKELEY STREET
		STREET 2:		STE 1650
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02116

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>0001286397</rptOwnerCik>
            <rptOwnerName>CARTHY MARK</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>222 BERKELEY ST.</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</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>2006-01-13</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>279</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.74</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>279</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/ Mark P. Carthy</signatureName>
        <signatureDate>2006-01-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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