SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549





Form 10-K/A





(Mark One)

|x | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

For the fiscal year ended September 30, 2008

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 0-18603





INTEGRAL SYSTEMS, INC.

(Exact Name of Registrant as specified in its
charter)







|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|MARYLAND                                                       |  | 52-1267968                          
|(State or other jurisdiction of incorporation or organization) |  | (I.R.S. Employer Identification No.)

5000 PHILADELPHIA WAY, LANHAM, MD 20706

(Address of principal executive offices and Zip Code)

Registrants telephone number, including area code:

(301) 731-4233

Securities registered pursuant to Section 12(b) of the Securities Exchange Act:

Common Stock, $.01 par value

Securities registered pursuant to
Section 12(g) of the Securities Exchange Act:

None





Indicate by a check mark if the Registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act of
1933.    Yes   ̈    No  x

Indicate by a check mark if the Registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Securities Exchange Act of 1934.    Yes   ̈    No  x

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 a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of large accelerated filer, accelerated filer, and smaller reporting company in
Rule 12b-2 of the Securities Exchange Act of 1934.



| |  |                            |  |                      |  |                          |  |                             
| |  | -------------------------- |  | -------------------- |  | ------------------------ |  | ----------------------------
| |  | Large accelerated filer   ̈ |  | Accelerated filer  x |  | Non-accelerated filer   ̈ |  | Smaller reporting company   ̈

Indicate by a check mark whether the registrant is a shell company (as defined in Rule 12b-2
of the Exchange Act of 1934).    Yes   ̈    No  x

The aggregate market value of the voting stock held by non-affiliates of the Registrant, based on the closing price on March 31, 2008, the last
business day of the Registrants most recently completed second fiscal quarter, as reported on the NASDAQ National Market System, was approximately $246.2 million. Shares of common stock held by each officer and director have been excluded from
this computation in that such persons may be deemed to be affiliates. This amount is provided only for purposes of this report on Form 10-K and does not represent an admission by the Registrant or any such person as to the status of such
person.

As of December 17, 2008, the Registrant had issued and outstanding 17,250,334 shares of common stock.

DOCUMENTS INCORPORATED BY REFERENCE

Portions of the Registrants definitive proxy statement for the 2009 Annual Meeting of Stockholders to be filed within 120 days after the Registrants fiscal year ended September 30, 2008, are incorporated by reference
into Part III of this Annual Report on Form 10-K.









---

EXPLANATORY NOTE

Integral Systems, Inc. hereby amends its Annual Report on Form 10-K for the fiscal year ended September 30, 2008 filed with the Securities and Exchange Commission on December 24, 2008 to correct the
disclosure regarding equity compensation plan information set forth under Item 12 of Part III.



---

PART III



|Item 12. | SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS
|-------- | ----------------------------------------------------------------------------------------------

Equity Compensation Plan Information

The following table sets forth certain equity compensation plan
information as of September 30, 2008 regarding equity compensation plans approved and not approved by our stockholders (shares in thousands):



|                                                           |  |                                                                                             |  |                                                                             |       |                                                                                                                                            |      
|---------------------------------------------------------- |  | ------------------------------------------------------------------------------------------- |  | --------------------------------------------------------------------------- | ----- | ------------------------------------------------------------------------------------------------------------------------------------------ | -----
|Plan Category                                              |  | Number of securities to beissued upon exercise ofoutstanding options,warrants and rights(a) |  | Weighted-averageexercise price ofoutstanding options,warrants and rights(b) |       | Number of securities remainingavailable for future issuanceunder equity compensationplans
(excluding securitiesreflected in column (a))(c)
|Equity compensation plans approved by security holders (1) |  | 1,979                                                                                       |  | $                                                                           | 19.37 |                                                                                                                                            | 2,479
|Equity compensation plans not approved by security holders |  |                                                                                            |  |                                                                             |      |                                                                                                                                            |     
|Total                                                      |  | 1,979                                                                                       |  | $                                                                           | 19.37 |                                                                                                                                            | 2,479



|(1) | Reflects equity awards granted under the Integral Systems, Inc. 2008 Stock Incentive Plan, the 2002 Stock Option Plan and the 1988 Stock Option Plan and 679 thousand shares
reserved for issuance under the 2008 Stock Incentive Plan and 1.8 million shares reserved for issuance under the Employee Stock Purchase Plan, all as of September 30, 2008.
|--- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



---

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly
caused this report to be signed on its behalf by the undersigned, thereunto duly authorized, as of December 31, 2008.



INTEGRAL SYSTEMS, INC.By:

/s/ WILLIAM M. BAMBARGER, JR.William M. Bambarger, Jr.Chief Financial Officer(Principal Financial Officer and Principal Accounting
Officer)




---

EXHIBIT INDEX



|              |  |                                                                                                
|------------- |  | -----------------------------------------------------------------------------------------------
|ExhibitNumber |  | Description                                                                                    
|31.1          |  | Certification Pursuant to Rule 13a-14(a) Under the Securities Exchange Act of 1934, as amended.
|              | 
|31.2          |  | Certification Pursuant to Rule 13a-14(a) Under the Securities Exchange Act of 1934, as amended.