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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 WtY0GxL2T5ivtsM6Vmk4tA==

<SEC-DOCUMENT>0000950117-06-004884.txt : 20061221
<SEC-HEADER>0000950117-06-004884.hdr.sgml : 20061221
<ACCEPTANCE-DATETIME>20061221140145
ACCESSION NUMBER:		0000950117-06-004884
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20061219
FILED AS OF DATE:		20061221
DATE AS OF CHANGE:		20061221

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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			NORTHUP JAMES R
		CENTRAL INDEX KEY:			0001218969

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-12944
		FILM NUMBER:		061292581

	MAIL ADDRESS:	
		STREET 1:		131 OLD SETTLERS BLVD
		CITY:			ROUND ROCK
		STATE:			TX
		ZIP:			78669
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>rsr_13305.xml
<DESCRIPTION>FORM 3
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-12-19</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001218969</rptOwnerCik>
            <rptOwnerName>NORTHUP JAMES R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>LAUREL BROOK ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MIDDLEFIELD</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06455</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>President Metrology Division</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>17500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>13.30</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2007-10-23</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-10-23</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>35000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Exercisable over a four year period, in quarterly increments, commencing on the date noted.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>James R. Northup</signatureName>
        <signatureDate>2006-12-20</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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