JMP Securities Healthcare Conference October SAFE HARBOR PROVISIONS FOR FORWARD

JMP Securities Healthcare  Conference October 7, 2008 SAFE HARBOR PROVISIONS FOR FORWARD‐LOOKING STATEMENTS: Statements made during this presentation, the proxy statements filed with the Securities and Exchange Commission (“Commission”), communications to shareholders, press releases and oral statements made by our representatives that are not historical in nature, or that state our or management’s intentions, hopes, beliefs, expectations or predictions of the future, may constitute “forward‐looking statements” within the meaning of Section 21E of the Securities and Exchange Act of 1934, as amended. Forward‐looking statements can often be identified by the use of forward‐looking terminology, such as “could,” “should,” “will,” “will be,” “will lead,” “will assist,” “intended,” “continue,” “believe,” “may,” “expect,” “hope,” “anticipate,” “goal,” “forecast,” “plan,” or “estimate” or variations thereof or similar expressions. Forward‐looking statements are not guarantees of future performance. Forward‐looking statements involve risks, uncertainties and assumptions. It is important to note that any such performance and actual results, financial condition or business, could differ materially from those expressed in such forward‐looking statements. Factors that could cause or contribute to such differences include, but are not limited to, the risk factors discussed under “Risk Factors” in our Annual Report on Form 10‐K for fiscal year ended March 31, 2008, as well as factors discussed elsewhere in other reports and documents we file with the Commission. Other unforeseen factors not identified herein could also have such an effect. We undertake no obligation to update or revise forward‐looking statements to reflect changed assumptions, the occurrence of unanticipated events or changes in future operating results, financial condition or business over time unless required by law. Interested persons are urged to review the risks described under “Risk Factors” and in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” in our Annual Report on Form 10‐K for fiscal year ended March 31, 2008, as well as in our other public disclosures and filings with the Commission. Quality Systems: Company Snapshot Through our NextGen and QSI divisions, we develop and provide  computer‐based practice management, medical records, and e‐ business applications for U.S. medical and dental group practices The company derives most of its revenue and growth from physician  group business and its high functionality practice management  suites Quality Systems is managed with an eye toward pursuing organic  growth, while concurrently maintaining a strategy of aggressive  reinvestment in new product and service development initiatives Quality Systems has an industry‐leading track record of strong  financial and shareholder returns, and a dedication to the highest  corporate governance standards A Track Record of Success The growth strategy developed by the Quality Systems  management team has delivered results: We believe the company has been growing at a faster rate than the  industry average and taking market share from our competitors Our revenue stream is diversified, with two‐thirds of sales to mid‐sized  and large customers and the rest to smaller customers  The company has successfully leveraged its strength in the practice  management business into the emerging medical record market ○ Currently 75% of our customers buy products in both categories By investing in new products and services, we can anticipate  customers’ unique needs and provide the solutions they demand A Track Record of Success The results are evident in our ongoing financial performance  and track record of delivering shareholder value:  A nearly 400% stock price increase the past five years Financial results that rank Quality Systems among the most  profitable companies and strongest cash flow generators in its  sector during the same period Solid first‐quarter FY’09 earnings that included a 31% jump in net  revenues and 40% increase in net income A corporate governance record predicated on pro‐shareholder  policies Industry Growth Drivers Growth Drivers Public Sector Initiatives HIPAA State / Local CCHIT                             Certification P4P Incentives Relaxation of Stark  Regulations  Technology Flexibility ROI Personal Health  Records (PHR) Purchaser Influence Payors Employers Quality Incentives Group Initiatives Organizational Map Corporate  Headquarters Irvine, CA NextGen Division 794 Employees Corporate  Admin. 44 Employees QSI Division 69 Employees Horsham, PA (Acq’d 1996) Atlanta, GA (Acq’d 1997) HSI St. Louis, MO (Acq’d 2008) Software Irvine, CA Depot Santa Ana, CA Experienced Management Team Title Steven Plochocki Chief Executive Officer, Quality Systems, Inc. Patrick Cline President, NextGen Healthcare, Quality Systems, Inc. Paul Holt Chief Financial Officer, Quality Systems, Inc. Donn Neufeld Executive Vice President and General Manager, Quality Systems, Inc. Fred Neufeld Executive Vice President and General Manager, NextGen Healthcare Scott Decker Senior Vice President, NextGen Healthcare Tim Eggena Executive Vice President, NextGen Practice Solutions, NextGen Healthcare Years of Industry Experience 36 27 13 28 30 12 15 Quality Systems Today  June 30, 2008 TTM Revenue: $199.7mm EPS: $1.55 TTM Revenue: Markets Served: $183.6mm (92% of total) Physicians • Practice Management • EMR • EDI • Revenue Cycle Management 1,160 Horsham, PA; Atlanta, GA; St. Louis, MO; Dallas, TX 794 TTM Revenue: Markets Served: $16.1mm (8% of total) Dentists • Practice Management • EPR • EDI 249 Irvine, CA; Santa Ana, CA 69 Billing Sites (6/30/08): Locations: Employees (6/30/08): Billing Sites (6/30/08): Locations: Employees (6/30/08): Product / Market Dynamics High Growth EMR Clinical Dental Growth EDI/ Connectivity MPM Low Growth Dental PM High Penetration Penetration Opportunity Low Penetration New vs. Recurring Revenue QSI Division New 25% Recurring 75% NextGen Division Recurring 43% New 57% Company Recurring 46% New 54% NextGen Healthcare  Current State of Adoption 5% Complete 5% Partial 10% Complete 10% Partial 1% Complete 49% Partial 90% Paper 80% Paper 50% Paper Small Practices Large Practices Hospital Outpatient Depts Inpatient Critical Care Ambulatory Care Acute Care Source: The Coker Group – 8/1/08 Quarterly Results – Revenue/EPS Note: Charges for adoption of SFAS 123R began in June 2006 quarter Our Strategy Is Working Revenue $200 $180 $160 $140 $120 $100 $80 $60 $40 $20 $0 Revenue (in thousands) 3/31/03 3/31/04 3/31/05 3/31/06 3/31/07 3/31/08 Earnings Per Share $1.60 $1.40 $1.20 $1.00 EPS $0.80 $0.60 $0.40 $0.20 $0.00 3/31/2003 3/31/2004 3/31/05 3/31/2006 3/31/2007 3/31/2008 Our Strategy is Working Cash Flow from Operations $45 Cash Flow from Ops (in thousands) $40 $35 $30 $25 $20 $15 $10 $5 $0 3/31/03 3/31/04 3/31/05 3/31/06 3/31/07 3/31/08 Net Income Margin 25.0% Net Income Margin 20.0% 15.0% 10.0% 5.0% 0.0% 3/31/03 3/31/04 3/31/05 3/31/06 3/31/07 3/31/08 Ongoing Strong Financial Performance Maintenance Revenues $60 $50 Maintenance (in thousands) $40 $30 $20 $10 $0 3/31/03 3/31/04 3/31/05 3/31/06 3/31/07 3/31/08 System Sales $90 $80 System Sales (in thousands) $70 $60 $50 $40 $30 $20 $10 $0 3/31/03 3/31/04 3/31/05 3/31/06 3/31/07 3/31/08 We Are Generating Meaningful  Results for Shareholders Awards & Honors • Forbes named QSI to the 200 Best Small Companies list for seven consecutive years – #5 in 2007 Quality Systems Highlights • Fortune list of 100 Fastest Growing Small Public Companies – #41 in 2007 • Business Week’s list of 100 Hot Growth Companies – #19 in 2007 • Business 2.0 list of 100 Fastest Growing Technology Companies – #78 in 2007 • #1 Rating – 2007/2008 -AC Group – EMR/EHR for multi-specialty, community health, FQHC’s, large, mid-size, and small practice categories • TEPR awards at 2001, 2002, 2003, 2004 conferences NextGen Highlights • HIMSS/HUG awards at 2003, 2004, 2005, 2006, 2007 and 2008 conferences — — — — Administrative / Financial Systems Clinical / Patient Information Systems Interoperability / RHIO Disease Surveillance • Expanded trade journal coverage: Healthcare Informatics, Health Data Management, Health Management Technology, Modern Healthcare Future Vision Maximize top/bottom line growth at NextGen and  EDI/Connectivity Maximize profit at QSI Division Stepped investments in Sales, Marketing, Implementation, Support  and Development Continued improvements – compensation and process HSI acquisition expands revenue cycle management division  service capabilities Prioritize organic growth – selectively evaluate inbound acquisition  opportunities Market share Niche products Channel expansion Investment Highlights Proven Growth and Profitability • Track record of organic growth and profitability – 5 year revenue CAGR of 28% and Net Income CAGR of 42% – most profitable company in market segment with 30%+ EBITDA margins • Self-funded, highly profitable growth strategy – recurring revenue base provides stable cash flow • Forbes list of Best 200 Small Companies seven consecutive years • $85 million NextGen sales pipeline @ 6/30/08 Robust Sales Pipeline Substantial Customer Base • Over 1,400 billing sites • Substantial cross-selling opportunities • Relationships with key health care institutions • NextGen products awarded top honors at HIMSS and TEPR trade shows • Ranked highly by AC Group and KLAS • Scalable technology platform with significant adoption in mid/large physician practices • Increasing focus on technology benefits in healthcare • Stark law relaxation • Pay for Performance initiatives • 7+ years working collaboratively as a management team Leading Suite of HCIT Products Positive HCIT Industry Trends Experienced Management Team Equity Profile (NASDAQ: QSII) as of 6/30/08 Recent Price Book Value Cash & marketable securities P/E – LTM Incl. cash & marketable securities P/E – LTM Excl. cash & marketable securities Market cap Shares Outstanding (FD) $1.1B 27.8M 24.0 $40.00/share $4.57/share $2.86/share 25.8

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