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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 
 FORM 10-K/A
 Amendment No. 1
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    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For The Fiscal Year Ended December 31, 2005
 OR
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    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the transition period from          to          .
 Commission File No. 1-13317
 DOT HILL SYSTEMS CORP.
  Delaware
    
    13-3460176(State or other jurisdiction of
    
    (I.R.S. Employerincorporation or organization)
    
    Identification No.)
 2200 Faraday Avenue, Suite 100Carlsbad, California
    
    92008(Address of principal executive offices)
    
    (Zip Code)
 (760) 931-5500
 Common Stock, $0.001 par value
 NONE
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   DOCUMENTS INCORPORATED BY REFERENCE




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TABLE OF CONTENTS  PART IIItem 9A. Controls and ProceduresPART IVItem 15. Exhibits and Financial Statement SchedulesSIGNATURESEXHIBIT 31.3EXHIBIT 31.4EXHIBIT 32.2    Table of Contents  DOT HILL SYSTEMS CORP.
 EXPLANATORY NOTE
 Controls and Procedures
 
 PART II
 
 Item 9A. Controls and Procedures
   Dot Hill Systems Corp.s Report on Internal Control Over Financial Reporting
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PART IV
 
 Item 15. Exhibits and Financial Statement Schedules
   ExhibitNumber2.1
    
    Agreement and Plan of Merger dated as of February 23, 2004, by and among Dot Hill Systems Corp., DHSA
Corp., Chaparral Network Storage, Inc., and C. Timothy Smoot, as Stockholders Representative.(1)3.1
    
    Certificate of Incorporation of Dot Hill Systems Corp.(2)3.2
    
    By-laws of Dot Hill Systems Corp.(2)4.1
    
    Certificate of Incorporation Dot Hill Systems Corp.(2)4.2
    
    By-laws of Dot Hill Systems Corp.(2)4.3
    
    Form of Common Stock Certificate.(3)4.4
    
    Certificate of Designation of Series A Junior Participating Preferred Stock, as filed with the
Secretary of State of Delaware on May 19, 2003.(4)4.5
    
    Form of Rights Certificate.(4)4.6
    
    Warrant to Purchase Shares of Common Stock dated May 24, 2002.(5)4.7
    
    Common Stock Warrant dated December 19, 2002.(5)4.8
    
    Warrant to Purchase Shares of Common Stock dated February 14, 2003.(5)4.9
    
    Common Stock Warrant dated March 14, 2003.(5)10.1
    
    Product Purchase Agreement between Dot Hill Systems Corp. and Sun Microsystems, Inc. dated May 24,
2002.(6)10.2
    
    Product Supplement/ Award Letter for Blade Product under agreement with Sun Microsystems, Inc. dated
May 24, 2002.(6)10.3
    
    Product Supplement/ Award Letter for SCSI Product under agreement with Sun Microsystems, Inc. dated
May 24, 2002.(6)
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ExhibitNumber10.4
    
    Product Supplement/ Award Letter for FC Product under agreement with Sun Microsystems, Inc. dated May
24, 2002.(6)10.5
    
    Second Amendment to Product Purchase Agreement, dated as of January 26, 2004 by and among Sun
Microsystems, Inc., Sun Microsystems International B.V., Dot Hill Systems Corp. and Dot Hill Systems
B.V.(15)10.6
    
    Third Amendment to Product Purchase Agreement, dated as of March 22, 2004, by and among Sun
Microsystems, Inc., Sun Microsystems International B.V., Dot Hill Systems Corp. and Dot Hill Systems
B.V.(15)10.7
    
    Product Supplement/ Award Letter (SATA) by and between Sun Microsystems, Inc. and Dot Hill Systems
Corp. dated as of March 22, 2004.(15)10.8
    
    Rights Agreement dated as of May 19, 2003 by and between Dot Hill Systems Corp. and American Stock
Transfer and Trust Company.(4)10.9
    
    Employment letter agreement dated August 2, 1999 between Dot Hill Systems Corp. and James L.
Lambert.(7)10.10
    
    Employment letter agreement dated August 2, 1999 between Dot Hill Systems Corp. and Dana W
Kammersgard.(7)10.11
    
    Employment offer letter dated November 12, 1999 between Dot Hill Systems Corp. and Preston Romm.(7)10.12
    
    Lease for Dot Hill Systems Corp.s headquarters in Carlsbad, California dated June 9, 1993.(5)10.13
    
    2000 Amended and Restated Equity Incentive Plan.(8)10.14
    
    Form of Stock Option Agreement (Incentive and Non-statutory Stock Options) used in connection with
the 2000 Amended and Restated Equity Incentive Plan.(8)10.15
    
    Form of Stock Option Grant Notice used in connection with the 2000 Amended and Restated Equity
Incentive Plan.(8)10.16
    
    2000 Amended and Restated Employee Stock Purchase Plan.(9)10.17
    
    2000 Non-Employee Directors Stock Option Plan.(10)10.18
    
    Form of Stock Option Agreement used in connection with the 2000 Non-Employee Directors Stock Option
Plan.(10)10.19
    
    Credit Agreement dated July 1, 2004 by and between Dot Hill Systems Corp. and Wells Fargo Bank,
National Association.(11)10.20
    
    Revolving Line of Credit Note dated July 1, 2004 issued by Dot Hill Systems Corp. to Wells Fargo
Bank, National Association.(11)10.21
    
    Security Agreement and Addendum dated July 1, 2004 by and between Dot Hill Systems Corp. and Wells
Fargo Bank, National Association.(11)10.22
    
    Manufacturing Agreement between Dot Hill Systems Corp. and Solectron Corporation dated May 20,
2002.(12)10.23
    
    OEM Agreement between Dot Hill Systems Corp. and Infortrend Technology, Inc. dated May 20, 2002.(12)10.24
    
    2005 Executive Compensation Plan for James L. Lambert effective January 1, 2005.(13)10.25
    
    2005 Executive Compensation Plan for Dana Kammersgard effective January 1, 2005.(13)10.26
    
    2005 Executive Compensation Plan for Preston Romm effective January 1, 2005.(13)10.27
    
    Change of Control Agreement dated August 23, 2001 between Dot Hill Systems Corp. and James L.
Lambert.(14)10.28
    
    Change of Control Agreement dated August 23, 2001 between Dot Hill Systems Corp. and Dana
Kammersgard.(14)10.29
    
    Change of Control Agreement dated August 23, 2001 between Dot Hill Systems Corp. and Preston
Romm.(14)10.30
    
    Securities Purchase Agreement dated March 11, 2003 between Dot Hill Systems Corp. and each of the
purchasers listed on the signature pages thereto.(5)10.31
    
    Registration Rights Agreement dated March 11, 2003 between Dot Hill Systems Corp. and each of the
purchasers listed on the signature pages thereto.(5)10.32
    
    Registration Rights Agreement dated March 4, 2003 between Dot Hill Systems Corp. and each of the
individuals listed on the signature pages thereto.(5)10.33
    
    Amendment to Manufacturing Agreement between Dot Hill Systems Corp. and Solectron Corporation dated
April 5, 2005.(16)10.34
    
    Description of Amended and Restated Policy for Director Compensation.(17)10.35
    
    Lease Agreement by and between Dot Hill Systems Corp. and Equastone 2200 Faraday, LLC effective as of
September 1, 2005 and dated as of September 16, 2005.(18)10.36
    
    Fourth Amendment to Product Purchase Agreement dated September 26, 2005 by and among Sun
Microsystems, Inc., Sun Microsystems International B.V., Dot Hill Systems Corp. and Dot Hill Systems
B.V.(19)
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ExhibitNumber10.37
    
    Product Supplement/ Award Letter dated September 27, 2005 by and among Sun Microsystems, Inc., Sun
Microsystems International B.V., Dot Hill Systems Corp. and Dot Hill Systems B.V.(19)10.38
    
    Second Amendment to Manufacturing Agreement dated September 16, 2005 between Dot Hill Systems Corp.
and Solectron Corporation.(19)10.39
    
    Second Award Letter dated September 16, 2005 between Dot Hill Systems Corp. and Solectron
Corporation.(19)10.40
    
    Development and OEM Supply Agreement dated July 26, 2005 by and among Dot Hill Systems Corp., Dot
Hill Systems B.V., Network Appliance, Inc. and Network Appliance B.V.(19)10.41
    
    Product Supplement/ Award Letter dated October 20, 2005 by and among Sun Microsystems, Inc., Sun
Microsystems International B.V., Dot Hill Systems Corp. and Dot Hill Systems B.V.(24)*10.42
    
    Description of Accelerated Vesting of Options.(20)10.43
    
    Form of Indemnity Agreement.(21)10.44
    
    Patent Cross License dated December 29, 2005 between Dot Hill Systems Corp. and International
Business Machines Corporation.(24)*10.45
    
    Offer letter agreement dated February 22, 2006 between Dot Hill Systems Corp. and Patrick Collins.(22)10.46
    
    Consulting letter agreement effective March 1, 2006 and dated March 2, 2006 between Dot Hill Systems
Corp. and James L. Lambert.(23)10.47
    
    Description of 2006 Executive Compensation Plan.(23)21.1
    
    Subsidiaries of Dot Hill Systems Corp.(5)23.1
    
    Consent of Deloitte & Touche LLP.(24)24.1
    
    Power of Attorney. Reference is made to page 52.(24)31.1
    
    Certification pursuant to 17 CFR 240.13a-14(a) or 17 CFR 240.15d-14(a), as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.(24)31.2
    
    Certification pursuant to 17 CFR 240.13a-14(a) or 17 CFR 240.15d-14(a), as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.(24)31.3
    
    Certification pursuant to 17 CFR 240.13a-14(a) or 17 CFR 240.15d-14(a), as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.31.4
    
    Certification pursuant to 17 CFR 240.13a-14(a) or 17 CFR 240.15d-14(a), as adopted pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002.32.1
    
    Certification pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.(24)32.2
    
    Certification pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the
Sarbanes-Oxley Act of 2002.
 
 
    
    Indicates management or compensatory plan or arrangement required to be identified pursuant
to Item 15(b).*
    
    Confidential treatment has been requested with respect to certain portions of this exhibit.
Omitted portions have been filed separately with the SEC.(1)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on February 24, 2004
and incorporated herein by reference.(2)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on September 19,
2001 and incorporated herein by reference.(3)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on January 14, 2003
and incorporated herein by reference.(4)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on May 19, 2003 and
incorporated herein by reference.(5)
    
    Filed as an exhibit to our Annual Report on Form 10-K for the year ended December 31, 2002
and incorporated herein by reference.(6)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended June 30, 2002
and incorporated herein by reference.(7)
    
    Filed as an exhibit to our Annual Report on Form 10-K for the year ended December 31, 1999
and incorporated herein by reference.(8)
    
    Filed as an exhibit to our Current Report on Form 8-K dated August 23, 2000 and incorporated
herein by reference.(9)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended June 30, 2004
and incorporated herein by reference.(10)
    
    Filed as an exhibit to our Registration Statement on Form S-8 (No. 333-43834) and
incorporated herein by reference.(11)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended September 30,
2004 and incorporated herein by reference. 5




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(12)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended June 30, 2002
and incorporated herein by reference.(13)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on February 9, 2005
and incorporated herein by reference.(14)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended September 30,
2001 and incorporated herein by reference.(15)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended March 31, 2004
and incorporated herein by reference.(16)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended June 30, 2005
and incorporated herein by reference.(17)
    
    Incorporated herein by reference to the description contained in our Current Report on Form
8-K filed with the SEC on July 29, 2005.(18)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on September 21,
2005 and incorporated herein by reference.(19)
    
    Filed as an exhibit to our Quarterly Report on Form 10-Q for the quarter ended September 30,
2005 and incorporated herein by reference.(20)
    
    Incorporated herein by reference to the description contained in our Current Report on Form
8-K filed with the SEC on December 7, 2005.(21)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on December 13, 2005
and incorporated herein by reference.(22)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on February 24, 2006
and incorporated herein by reference.(23)
    
    Filed as an exhibit to our Current Report on Form 8-K filed with the SEC on March 8, 2006 and
incorporated herein by reference.(24)
    
    Filed as an exhibit to our Annual Report on Form 10-K for the year ended December 31, 2005
and incorporated herein by reference. 6




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SIGNATURES
  DOT HILL SYSTEMS CORP.Date: November 13, 2006By:
    
    /s/ Hanif I. JamalHanif I. JamalSenior Vice President and Chief Financial Officer
 7