<?xml version="1.0"?><ownershipDocument><schemaVersion>X0201</schemaVersion>    <documentType>4</documentType><periodOfReport>2004-01-22</periodOfReport><notSubjectToSection16>0</notSubjectToSection16><issuer><issuerCik>0001014672</issuerCik><issuerName>CALIPER TECHNOLOGIES CORP</issuerName>        <issuerTradingSymbol>CALP</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId><rptOwnerCik>0001242976</rptOwnerCik><rptOwnerName>KNIGHTON JAMES L</rptOwnerName></reportingOwnerId><reportingOwnerAddress><rptOwnerStreet1>605 FAIRCHILD DRIVE</rptOwnerStreet1><rptOwnerStreet2></rptOwnerStreet2><rptOwnerCity>MOUNTAIN VIEW</rptOwnerCity><rptOwnerState>CA</rptOwnerState><rptOwnerZipCode>94043-2234</rptOwnerZipCode><rptOwnerStateDescription></rptOwnerStateDescription></reportingOwnerAddress><reportingOwnerRelationship><isDirector>0</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>CFO</officerTitle></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2004-01-22</value></transactionDate><deemedExecutionDate></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionTimeliness><value></value></transactionTimeliness><transactionAmounts><transactionShares><value>14000.0000</value></transactionShares><transactionPricePerShare><value>9.1900</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>19872.0000</value><footnoteId id="F1" /></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></nonDerivativeTransaction></nonDerivativeTable><derivativeTable><derivativeTransaction><securityTitle><value>Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>9.1900</value></conversionOrExercisePrice><transactionDate><value>2004-01-22</value></transactionDate><deemedExecutionDate></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionTimeliness><value></value></transactionTimeliness><transactionAmounts><transactionShares><value>14000.0000</value></transactionShares><transactionPricePerShare><value>9.1900</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2004-01-22</value><footnoteId id="F2" /></exerciseDate><expirationDate><value>2014-01-22</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>14000.0000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>14000.0000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">Includes 5,872 ESPP shares purchased on November 30, 2003.  Of the 14,000 shares, 100% of the shares vest on March 31, 2004.</footnote><footnote id="F2">100% of the shares subject to option vest on March 31, 2004.</footnote></footnotes><remarks></remarks><ownerSignature><signatureName>/s/ Anthony T. Hendrickson (Attorney in Fact)</signatureName><signatureDate>2004-01-23</signatureDate></ownerSignature></ownershipDocument>

