================================================================================ UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 --------------- FORM 10-K/A NO. 2 (Mark One) |X| ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended March 31, 2005 or |_| TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from ______________ to ______________ Commission file number: 0-13801 Quality Systems, Inc. (Exact name of Registrant as specified in its charter) California 95-2888568 (State or other jurisdiction of (I.R.S. Employer Identification No.) incorporation or organization) 18191 Von Karman Avenue, Suite 450, Irvine, California 92603 (Address of principal executive offices, including zip code) (949) 255-2600 (Registrant's telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: None None (Title of each class) (Name of each exchange on which registered) Securities registered pursuant to Section 12(g) of the Act: Common Stock, par value $.01 per Share (Title of class) Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the Registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes |X| No |_| Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of Registrant's knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. |_| Indicate by check mark whether the Registrant is an accelerated filer (as defined in Rule 12b-2 of the Act). Yes |X| No |_| The aggregate market value of the voting stock held by non-affiliates of the Registrant as of September 30, 2004: $210,543,000 (based on the closing sales price of the Registrant's Common Stock as reported in the NASDAQ National Market System on that date, $50.51 per share).* The aggregate market value of the voting stock held by non-affiliates of the Registrant as of June 3, 2005: $415,011,000 (based on the closing sales price of the Registrant's Common Stock as reported in the NASDAQ National Market System on that date, $51.30 per share).* *For purposes of this report, in addition to those shareholders which fall within the definition of "affiliates" under Rule 405 of the Securities Act of 1933, as amended, holders of ten percent or more of the Registrant's Common Stock are deemed to be affiliates. Indicate the number of shares outstanding of each of the Registrant's classes of Common Stock, as of the latest practicable date. Common Stock, $.01 par value 13,115,360 ---------------------------- ----------------------------- (Class) (Outstanding at June 8, 2005) DOCUMENTS INCORPORATED BY REFERENCE None. EXPLANATORY NOTE This Amendment No. 2 to Form 10-K is being filed to correct a typographical error contained on the signature page and power of attorney for the initial filing of the Registrant's Form 10-K. As originally filed, the signature page and the power of attorney contained on the signature page inadvertently included the conformed signature of Mr. Ahmed Hussein, one of the members of the Registrant's board of directors. However, Mr. Hussein did not sign the Form 10-K or power of attorney. ================================================================================ INDEX TO EXHIBITS EXHIBIT NUMBER EXHIBIT - ------ ------- 3.1 Articles of Incorporation of the Company, as amended, are hereby incorporated by reference to Exhibit 3.1 to the Company's Annual Report on Form 10-K for the year ended March 31, 1984, File No. 2-80056. 3.1.1 Amendment to Articles of Incorporation, effective March 4, 2005. ** 3.2 Bylaws of the Company, as amended and restated. ** 3.3 Certificate of Amendment of Bylaws of the Company is hereby incorporated by reference to Exhibit 3.2.1 to the Company's Registration Statement on Form S-1, File No. 333-00161. 3.4 Text of Sections 2 and 3 of Article II of the Bylaws of the Company is hereby incorporated By reference to Exhibit 3.2.2 to the Company's Quarterly report on Form 10-QSB for the period Ended December 31, 1996, File No. 0-13801. 3.5 Certificate of Amendment of Bylaws of the Company, is hereby incorporated by reference to Exhibit 3.2.3 to the Company's Annual Report on Form 10-K for the year ended March 31, 2000, File No. 0-13801. 10.2* 1989 Incentive Stock Option Plan is hereby incorporated by reference to Exhibit 4.1 to the Company's Registration Statement on Form S-8, File No. 33-31949. 10.2.1* Form of Incentive Stock Option Agreement is hereby incorporated by reference to Exhibit 10.2 to the Company's Registration Statement on Form S-1, File No. 333-00161. 10.2.2* Form of Non-Qualified Stock Option Agreement is hereby incorporated by reference to Exhibit 10.3 to the Company's Registration Statement on Form S-1, File No. 333-00161. 10.3* Form of Incentive Stock Option Agreement is hereby incorporated by reference to Exhibit 10.2 to the Company's Registration Statement on Form S-1, File No. 2-80056. 10.4* 1993 Deferred Compensation Plan is hereby incorporated by reference to Exhibit 10.5 to the Company's Annual Report on Form 10-KSB for the year ended March 31, 1994, File No. 0-13801. 10.4.2* Profit Sharing and Retirement Plan, as amended, is hereby incorporated by reference to Exhibit 10.4.2 to the Company's Annual Report on Form 10-KSB for the year ended March 31, 1994, File No. 0-13801. 3 EXHIBIT NUMBER EXHIBIT - ------ ------- 10.4.3* Profit Sharing and Retirement Plan, as amended, amendments No. 2 and 3, are hereby incorporated by reference to Exhibit 10.4.3 to the Company's Annual Report on Form 10-KSB for the year ended March 31, 1996, File No. 0-13801. 10.5 Series "A" Convertible Preferred Stock Purchase Agreement, as amended, dated April 21, 1995 between the Company and Clinitec International, Inc., is hereby incorporated by reference to Exhibit 10.11 to the Company's Annual Report on Form 10-KSB for the year ended March 31, 1995, File No. 0-13801. 10.6 Form of Indemnification Agreement is hereby incorporated by reference to Exhibit 10.10 to the Company's Registration Statement on Form S-1, File No. 333-00161. 10.6.1* Form of Indemnification Agreement for directors and executive officers authorized January 27, 2005. ** 10.7 Agreement and Plan of Merger, dated May 16, 1996, by and among Quality Systems, Inc., CII Acquisition Corporation, Clinitec International, Inc. and certain shareholders of Clinitec International, Inc. and certain exhibits are hereby incorporated by reference to Exhibit 2 to the Company's Current Report on Form 8-K, dated May 17, 1996 and filed May 30, 1996. 10.8 Asset Purchase Agreement, dated May 15, 1997, by and among NextGen Healthcare Information Systems, Inc., MHIS Acquisition Corp., Quality Systems, Inc., and certain shareholders of NextGen Healthcare Information Systems, Inc. is hereby incorporated by reference to Exhibit 2 of Company's Current Report on Form 8-K, dated May 15, 1997 and filed May 29, 1997, File No. 0-13801. 10.9* 1998 Employee Stock Contribution Plan is hereby incorporated by reference to Exhibit 4.1 to the Company's Registration Statement on Form S-8, File No. 333-63131. 10.10* 1998 Stock Option Plan is hereby incorporated by reference to Exhibit 4.1 to the Company's Registration Statement on Form S-8, File No. 333-67115. 10.10.1* Amended and Restated 1998 Stock Option Plan. ** 10.11* Memorandum of Understanding regarding the April 3, 2000 resignation of Sheldon Razin between Sheldon Razin and Quality Systems, Inc., is hereby incorporated by reference to Exhibit 10.16 to the Company's Annual Report on Form 10-K for the year ended March 31, 2000, File No. 0-13801. 10.12* Memorandum of Understanding Relating to Director Nominees is hereby incorporated by reference to Company's Definitive Proxy Statement for the Company's 1999 Shareholder's Meeting, File No. 001-12537. 4 EXHIBIT NUMBER EXHIBIT - ------ ------- 10.13* Employment Agreement dated July 20, 2000 between Quality Systems, Inc. and Lou Silverman is hereby incorporated by reference to Exhibit 10.18 to the Company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2000, File No. 0-13801. 10.14 Lease Agreement between Company and Tower Place, L.P. dated November 15, 2000, commencing February 5, 2001 is hereby incorporated by reference to Exhibit 10.14 to the Company's Annual Report on Form 10-K for the year ended March 31, 2001, File No. 0-13801. 10.15 Lease Agreement between Company and Orangewood Business Center Inc. dated April 3, 2000, amended February 22, 2001, is hereby incorporated by reference to Exhibit 10.15 to the Company's Annual Report on Form 10-K for the year ended March 31, 2001, File No. 0-13801. 10.16 Lease Agreement between Company and Craig Development Corporation dated February 20, 2001 is hereby incorporated by reference to Exhibit 10.16 to the Company's Annual Report on Form 10-K for the year ended March 31, 2001, File No. 0-13801. 10.17 Sublease Agreement between Company and Infinium Software dated February 22, 2002 is hereby incorporated by reference to Exhibit 10.17 to the Company's Annual Report on Form 10-K for the year ended March 31, 2003, File No. 0-13801. 10.18 Lease Agreement between Company and HUB Properties LLC dated May 8, 2002 is hereby incorporated by reference to Exhibit 10.18 to the Company's Annual Report on Form 10-K for the year ended March 31, 2003, File No. 0-13801. 10.19 Lease Agreement between the Company and LakeShore Towers Limited Partnership Phase IV, a California limited partnership, dated September 15, 2004. ** 10.20* Board Service Agreement between the Company and Lou Silverman is incorporated by reference to Exhibit 10.2.1 to our Current Report of Form 8-K, dated May 31, 2005, File No. 001-12537. 10.21* Board Service Agreement between the Company and Patrick Cline is incorporated by reference to Exhibit 10.2.1 to the Company's Current Report of Form 8-K, dated May 31, 2005, File No. 001-12537. 21 List of Subsidiaries**** 23.1 Consent of Independent Registered Public Accounting Firm - Grant Thornton LLP** 5 EXHIBIT NUMBER EXHIBIT - ------ ------- 24 Power of Attorney ***** 31.1 Certification of Chief Executive Officer Required by Rule 13a-14(a) of the Securities Exchange Act of 1934, as amended, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 *** 31.2 Certification of Chief Financial Officer Required by Rule 13a-14(a) of the Securities Exchange Act of 1934, as amended, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 *** 32.1 Certification of Chief Executive Officer and Chief Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. ** * This exhibit is a management contract or a compensatory plan or arrangement. ** Filed as an exhibit to the initial filing of this Report and incorporated herein by reference. *** Filed herewith. **** Filed as an exhibit to Amendment No. 1 to this Report. ***** Contained on the signature page to the initial filing of this Report, and corrected via the Explanatory Note on the facing page of this Form 10-K/A No. 2. 6 SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this Form 10-K/A No. 2 to be signed on its behalf by the undersigned, thereunto duly authorized. By: /s/ LOUIS E. SILVERMAN -------------------------- Louis E. Silverman, President and Chief Executive Officer Date: August 19, 2005 Pursuant to the requirement of the Securities Exchange Act of 1934, this Form 10-K/A No. 2 has been signed by the following persons on behalf of the registrant and in the capacities and on the dates indicated. Signature Title Date - ----------------------------- ---------------------------------------- --------------- /s/ SHELDON RAZIN* Chairman of the Board August 19, 2005 - ----------------------------- Sheldon Razin /s/ LOUIS E. SILVERMAN Director, President and Chief Executive - ----------------------------- Officer (Principal Executive Louis E. Silverman Officer)/Director August 19, 2005 /s/ PATRICK CLINE* Director, President, NextGen Healthcare - ----------------------------- Information Systems Division August 19, 2005 Patrick Cline /s/ PAUL HOLT Secretary and Chief Financial Officer - ----------------------------- (Principal Financial Officer) August 19, 2005 Paul Holt /s/ WILLIAM BOTTS* Director August 19, 2005 - ----------------------------- William Botts /s/ MAURICE DEWALD* Director August 19, 2005 - ----------------------------- Maurice DeWald - ----------------------------- Director August 19, 2005 Ahmed Hussein /s/ JONATHAN JAVITT* Director August 19, 2005 - ----------------------------- Jonathan Javitt /s/ VINCENT LOVE* Director August 19, 2005 - ----------------------------- Vincent Love /s/ STEVEN PLOCHOCKI* Director August 19, 2005 - ----------------------------- Steven Plochocki *By: /S/ LOUIS E. SILVERMAN ------------------------ Louis E. Silverman, Attorney-In-Fact 7 INDEX TO EXHIBITS FILED WITH THIS FORM 10-K/A NO. 2 EXHIBIT NUMBER EXHIBIT - ------ ------- 31.1 Certification of Chief Executive Officer Required by Rule 13a-14(a) of the Securities Exchange Act of 1934, as amended, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. 31.2 Certification of Chief Financial Officer Required by Rule 13a-14(a) of the Securities Exchange Act of 1934, as amended, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. 8