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

    <documentType>4</documentType><periodOfReport>2004-01-09</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>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>23</value></transactionShares><transactionPricePerShare><value>1.4062</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>55750</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By Trust</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>63227</value></transactionShares><transactionPricePerShare><value>2.50</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>118977</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By Trust</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>14506</value></transactionShares><transactionPricePerShare><value>3.25</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>133483</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By Trust</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>F</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>9316</value></transactionShares><transactionPricePerShare><value>15.71</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>124167</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By Trust</value></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>F</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>3749</value></transactionShares><transactionPricePerShare><value>15.71</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>101944</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeHolding><securityTitle><value>Common Stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>79180</value><footnoteId id="F5"/></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By 401(k) Plan</value></natureOfOwnership></ownershipNature></nonDerivativeHolding></nonDerivativeTable><derivativeTable><derivativeTransaction><securityTitle><value>Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>1.4062</value></conversionOrExercisePrice><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>23</value></transactionShares><transactionPricePerShare><footnoteId id="F4"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2001-03-20</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2011-03-20</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>23</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>63227</value></transactionShares><transactionPricePerShare><footnoteId id="F4"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2000-01-27</value><footnoteId id="F2"/></exerciseDate><expirationDate><value>2006-06-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>63227</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>1540</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>3.25</value></conversionOrExercisePrice><transactionDate><value>2004-01-09</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>14506</value></transactionShares><transactionPricePerShare><footnoteId id="F4"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2002-04-29</value><footnoteId id="F3"/></exerciseDate><expirationDate><value>2012-04-29</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>14506</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>72260</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">The shares subject to the option vest daily and ratably over a period of two years beginning March 20, 2001.</footnote><footnote id="F2">The shares subject to the option vest daily and ratable over a period of four years beginning January 27, 2000.</footnote><footnote id="F3">The shares subject to the option vest daily and ratable over a period of four years beginning April 29, 2002.</footnote><footnote id="F4">Not Applicable</footnote><footnote id="F5">Between July 1, 2003 and December 31, 2003, 2,333 shares of Common Stock were transferred to the Cypress Bioscience, Inc. 401(k) plan, of which the Reporting Person is the trustee and has voting power over such shares.</footnote></footnotes><remarks/><ownerSignature><signatureName>Sabrina Martucci Johnson Attorney-in-Fact</signatureName><signatureDate>2004-01-13</signatureDate></ownerSignature></ownershipDocument>

