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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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<SEC-DOCUMENT>0001181431-06-052285.txt : 20060912
<SEC-HEADER>0001181431-06-052285.hdr.sgml : 20060912
<ACCEPTANCE-DATETIME>20060912110652
ACCESSION NUMBER:		0001181431-06-052285
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060911
FILED AS OF DATE:		20060912
DATE AS OF CHANGE:		20060912

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			MERCURY COMPUTER SYSTEMS INC
		CENTRAL INDEX KEY:			0001049521
		STANDARD INDUSTRIAL CLASSIFICATION:	ELECTRONIC COMPONENTS & ACCESSORIES [3670]
		IRS NUMBER:				042741391
		STATE OF INCORPORATION:			MA
		FISCAL YEAR END:			0630

	BUSINESS ADDRESS:	
		STREET 1:		199 RIVERNECK RD
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824
		BUSINESS PHONE:		9782561300

	MAIL ADDRESS:	
		STREET 1:		199 RIVERNECK ROAD
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			SALINE CRAIG A
		CENTRAL INDEX KEY:			0001274409

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-23599
		FILM NUMBER:		061085638
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>rrd129978.xml
<DESCRIPTION>OPTION EXCHANGE
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-09-11</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001049521</issuerCik>
        <issuerName>MERCURY COMPUTER SYSTEMS INC</issuerName>
        <issuerTradingSymbol>MRCY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001274409</rptOwnerCik>
            <rptOwnerName>SALINE CRAIG A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>5 FORBES LANE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>ANDOVER</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01810</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Sr. VP, Org Development</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-09-11</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>23431</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>26.96</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-09-11</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>40000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-01-13</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-01-13</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>40000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">On September 11, 2006, Mercury Computer Systems, Inc., cancelled, pursuant to its option exchange program, an option granted to the reporting person on January 13, 2004.  In exchange for the option, the reporting person received a restricted stock award covering 10,000 shares which vests as to two-thirds of the covered shares on September 11, 2008 and one-third of the covered shares on September 11, 2009.</footnote>
        <footnote id="F2">The cancelled option provided for vesting in four equal installments commencing on January 13, 2005.</footnote>
        <footnote id="F3">Field N/A to this transaction but was completed to allow for electronic filing only.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Craig Barrows, Attorney-in-fact</signatureName>
        <signatureDate>2006-09-12</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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