<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-09-11</periodOfReport>
    <issuer>
        <issuerCik>0000716054</issuerCik>
        <issuerName>CYPRESS BIOSCIENCE INC</issuerName>
        <issuerTradingSymbol>cypb</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001055666</rptOwnerCik>
            <rptOwnerName>KRANZLER JAY D</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>1</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>CEO and Secretary</officerTitle></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2003-09-11</value></transactionDate><transactionCoding><transactionFormType>5</transactionFormType><transactionCode>G</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>5000</value><footnoteId id="F1"/></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>35485</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By Trust</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeHolding><securityTitle><value>Common Stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>105693</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeHolding><nonDerivativeHolding><securityTitle><value>Common Stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>76847</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By 401(k) Plan</value><footnoteId id="F2"/></natureOfOwnership></ownershipNature></nonDerivativeHolding></nonDerivativeTable><footnotes><footnote id="F1">Gift to an organization not affilitated with the Reporting Person.</footnote><footnote id="F2">Between June 1, 2002 and June 30, 2003, the reporting person acquired 34,921 shares of Cypress Bioscience, Inc. Common Stock under the Cypress Bioscience, Inc. 401(k) plan.</footnote></footnotes><remarks/><ownerSignature><signatureName>Sabrina Martucci Johnson Attorney-in-Fact</signatureName><signatureDate>2003-09-17</signatureDate></ownerSignature></ownershipDocument>

