-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 Okd68XTcbPPiBwimSAMCcQGeODXcAdNr6FqmRGDwRLEAUg7NGZhbboP//Bu3ggRH
 CJfo/SkGfa9PJtTcDI/2uw==

<SEC-DOCUMENT>0001012975-06-000015.txt : 20060118
<SEC-HEADER>0001012975-06-000015.hdr.sgml : 20060118
<ACCEPTANCE-DATETIME>20060118191254
ACCESSION NUMBER:		0001012975-06-000015
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:			FAMBROUGH DOUGLAS
		CENTRAL INDEX KEY:			0001259856

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		06536573

	BUSINESS ADDRESS:	
		STREET 1:		222 BERKELEY STREET
		STREET 2:		SUITE 1650
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02116
		BUSINESS PHONE:		6173577474

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>0001259856</rptOwnerCik>
            <rptOwnerName>FAMBROUGH DOUGLAS</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O OXFORD BIOSCIENCE PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>222 BERKELEY ST.</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></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>1559</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.74</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1559</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/ Douglas Fambrough</signatureName>
        <signatureDate>2006-01-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----