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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 NyzLEXuhrJveyFbm+xXpAI9IvUdJaBRlWoNVcUd3Sz2MVeqUCoqIT2kLJpaMio0q
 gqOqNL1nPDnZ/F5O6sYYug==

<SEC-DOCUMENT>0001252291-03-000002.txt : 20030910
<SEC-HEADER>0001252291-03-000002.hdr.sgml : 20030910
<ACCEPTANCE-DATETIME>20030910084852
ACCESSION NUMBER:		0001252291-03-000002
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030908
FILED AS OF DATE:		20030910

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			MUMOLA PETER
		CENTRAL INDEX KEY:			0001252291

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-12944
		FILM NUMBER:		03888958

	BUSINESS ADDRESS:	
		STREET 1:		ZYGO CORP
		STREET 2:		LAUREL BROOK RD
		CITY:			MIDDLEFIELD
		STATE:			CT
		ZIP:			06455
		BUSINESS PHONE:		8603478506

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ZYGO CORP
		CENTRAL INDEX KEY:			0000730716
		STANDARD INDUSTRIAL CLASSIFICATION:	OPTICAL INSTRUMENTS & LENSES [3827]
		IRS NUMBER:				060864500
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			0630

	BUSINESS ADDRESS:	
		STREET 1:		LAUREL BROOK RD
		CITY:			MIDDLEFIELD
		STATE:			CT
		ZIP:			06455
		BUSINESS PHONE:		8603478506

	MAIL ADDRESS:	
		STREET 1:		LAUREL BROOK ROAD
		CITY:			MIDDLEFIELD
		STATE:			CT
		ZIP:			06455
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>primary_doc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>

<ownershipDocument>

    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2003-09-08</periodOfReport>


    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0000730716</issuerCik>
        <issuerName>ZYGO CORP</issuerName>
        <issuerTradingSymbol>ZIGO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001252291</rptOwnerCik>
            <rptOwnerName>MUMOLA PETER</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>110 RIVERVIEW DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GUILFORD</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06437</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>VP, Optics Division</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>

        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.54</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2003-09-08</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>4500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2003-08-26</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2012-08-26</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>

    </derivativeTable>

    <footnotes>
        <footnote id="F1">Reporting Person ceased to be an employee of Zygo Corporation after September 5, 2003. Pursuant to the terms of the option agreement, the options are no longer exercisable.</footnote>
        <footnote id="F2">Employee stock option was exercisable over a four year period, in quarterly increments, commencing on the date noted.</footnote>
    </footnotes>


    <ownerSignature>
        <signatureName>Peter B. Mumola</signatureName>
        <signatureDate>2003-09-10</signatureDate>
    </ownerSignature>

</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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