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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 GrW+ScSqwwSolcVNzeMURStT19i+1XkoUIzqKEtX16sAWPrut7qDiroSSRym5Xvh
 zEf/9ZLstlwaUM2iqqyTnw==

<SEC-DOCUMENT>0000077551-03-000050.txt : 20030904
<SEC-HEADER>0000077551-03-000050.hdr.sgml : 20030904
<ACCEPTANCE-DATETIME>20030904165033
ACCESSION NUMBER:		0000077551-03-000050
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030902
FILED AS OF DATE:		20030904

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			SMITH ORIN R
		CENTRAL INDEX KEY:			0001188423

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-04389
		FILM NUMBER:		03881929

	MAIL ADDRESS:	
		STREET 1:		PO BOX 717
		STREET 2:		--
		CITY:			BRIELLE
		STATE:			NJ
		ZIP:			08730

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			APPLERA CORP
		CENTRAL INDEX KEY:			0000077551
		STANDARD INDUSTRIAL CLASSIFICATION:	LABORATORY ANALYTICAL INSTRUMENTS [3826]
		IRS NUMBER:				061534213
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			0630

	BUSINESS ADDRESS:	
		STREET 1:		301 MERRITT 7
		CITY:			NORWALK
		STATE:			CT
		ZIP:			06851
		BUSINESS PHONE:		2038402000

	MAIL ADDRESS:	
		STREET 1:		301 MERRITT 7
		CITY:			NORWALK
		STATE:			CT
		ZIP:			06851

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	PE CORP
		DATE OF NAME CHANGE:	19990129

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	PERKIN ELMER CORP
		DATE OF NAME CHANGE:	19930601
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-09-02</periodOfReport>
    <issuer>
        <issuerCik>0000077551</issuerCik>
        <issuerName>APPLERA CORP</issuerName>
        <issuerTradingSymbol>ABI/CRA</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001188423</rptOwnerCik>
            <rptOwnerName>SMITH ORIN R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>APPLERA CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>301 MERRITT 7</rptOwnerStreet2>
            <rptOwnerCity>NORWALK</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06851-1070</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Applied Biosystems Group Common Stock Units</value></securityTitle><transactionDate><value>2003-09-02</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>387.2</value></transactionShares><transactionPricePerShare><value>22.22</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>17506.52</value><footnoteId id="F1"/></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><nature
OfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Celera Genomics Group Common Stock Units</value></securityTitle><transactionDate><value>2003-09-02</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>135.51</value></transactionShares><transactionPricePerShare><value>10.305</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>4624.81</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeHolding><securi
tyTitle><value>Applied Biosystems Group Common Stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>4000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeHolding><nonDerivativeHolding><securityTitle><value>Celera Genomics Group Common Stock</value></securityTitle><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeHolding></nonDerivativeTable><footnotes><footnote id="F1">Includes 38.60 Applied Biosystems Group Common Stock Units acquired in July 2003 pursuant to the dividend reinvestment feature of the Company's director stock purchase and stoc
k incentive plans.</footnote></footnotes><remarks/><ownerSignature><signatureName>Thomas P. Livingston, Attorney-in-Fact for Orin R. Smith</signatureName><signatureDate>2003-09-04</signatureDate></ownerSignature></ownershipDocument>

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</SEC-DOCUMENT>
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