-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 KpEt3VfLUFv7LbNekiJGHHzt/DQjRh9GbZj+XXsa1n+4GzirGShCJvjaunAEBcrH
 OGEQ4TsClKkTYbUP9N0SjQ==

<SEC-DOCUMENT>0000716054-08-000004.txt : 20080104
<SEC-HEADER>0000716054-08-000004.hdr.sgml : 20080104
<ACCEPTANCE-DATETIME>20080104135158
ACCESSION NUMBER:		0000716054-08-000004
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20080102
FILED AS OF DATE:		20080104
DATE AS OF CHANGE:		20080104

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			CYPRESS BIOSCIENCE INC
		CENTRAL INDEX KEY:			0000716054
		STANDARD INDUSTRIAL CLASSIFICATION:	BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
		IRS NUMBER:				222389839
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		4350 EXECUTIVE DRIVE,SUITE 325
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		8584522323

	MAIL ADDRESS:	
		STREET 1:		4350 EXECUTIVE DRIVE,SUITE 325
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	IMRE CORP
		DATE OF NAME CHANGE:	19920703

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			WHEELER DENISE
		CENTRAL INDEX KEY:			0001279110

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-12943
		FILM NUMBER:		08510650

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		858-452-2323

	MAIL ADDRESS:	
		STREET 1:		4350 EXECUTIVE DR
		STREET 2:		STE 325
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

	FORMER NAME:	
		FORMER CONFORMED NAME:	WOOLARD DENISE
		DATE OF NAME CHANGE:	20040206
</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>2008-01-02</periodOfReport>

    <issuer>
        <issuerCik>0000716054</issuerCik>
        <issuerName>CYPRESS BIOSCIENCE INC</issuerName>
        <issuerTradingSymbol>CYPB</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001279110</rptOwnerCik>
            <rptOwnerName>WHEELER DENISE</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>4350 EXECUTIVE DRIVE SUITE 325</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>General Counsel</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>11.03</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-01-02</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>47723</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-01-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>47723</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>47723</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The shares subject to the option shall vest daily and ratably over four years from the date of grant, such that the option shall be fully vested on January 2, 2012.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Sabrina Martucci Johnson Attorney-in-Fact</signatureName>
        <signatureDate>2008-01-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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