UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-K/A

AMENDMENT NO. 2

(Mark One)

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

For the fiscal year ended June 30, 2012

o 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: 1-10768

MEDIWARE INFORMATION SYSTEMS, INC.

(Exact name of registrant as specified in its charter)

New York	11-2209324
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

11711 West 79th Street Lenexa, KS	66214
(Address of principal executive offices)	(Zip Code)

Registrant's telephone number, including area code: (913) 307-1000

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

Title of each class		Name of each exchange on which registered
Common Stock, par value $ .10 per share		Nasdaq Capital Market

Securities registered pursuant to Section 12(g) of the Act: None

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

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes o No ý

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 ý No o

Indicate by check mark whether the registrant has submitted electronically and posted on its Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes ý No o

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Registration 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 the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer	o	Accelerated Filer	o

Non-accelerated filer	o	Smaller reporting company	ý
(Do not check if a smaller reporting company)

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

The aggregate market value of the voting stock held by non-affiliates of the registrant, based upon the closing sales price of its common stock on December 31, 2011 as reported on the Nasdaq Capital Market, was approximately $66,089,000.

The number of shares outstanding of the registrant's common stock, as of August 31, 2012, was 8,496,966 shares.

DOCUMENTS INCORPORATED BY REFERENCE

NONE

The purpose of this Amendment No. 2 is to correct a second printer error regarding Exhibit 101 (XBRL interactive data) to our Annual Report on Form 10-K. That Amendment No. 1 was filed in part to submit Exhibit 101 to correct a printer error regarding Note 5 and Note 14 in the Notes to our Consolidated Financial Statements that was contained within Exhibit 101 to the Annual Report on Form 10-K. This Amendment No. 2 also updates the exhibit index to reflect the Exhibit 101 and certifications filed together with this Amendment No. 2.

PART IV

Item 15. Exhibits and Financial Statement Schedules.

EXHIBIT INDEX

3.1	Restated Certificate of Incorporation.	Incorporated by reference to Exhibit 4 to the Registration Statement on Form S-8, filed on July 3, 1996.
3.2	Certificate of Amendment of the Certificate of Incorporation.	Incorporated by reference to Exhibit 4.2 to the Registration Statement on Form S-8, filed on October 4, 2004.
3.3	By-laws	Incorporated by reference to Exhibit 3.3 to the Annual Report on Form 10-K, filed September 7, 2011.
10.5	Form 2003 Mediware Information Systems, Inc. Equity Incentive Plan Stock Option Plan Agreement.	Incorporated by reference to Exhibit 10.13 to the Annual Report on Form 10-K, filed on September 2, 2005.
10.6	Form of Amendment to 2003 Mediware Information Systems, Inc. Equity Incentive Plan Stock Option Agreement.	Incorporated by reference to Exhibit 10.58 to the Current Report on Form 8-K, filed on March 25, 2005.
10.7	Employment Agreement dated as of April 18, 2003 between Mediware Information Systems, Inc. and Robert Tysall-Blay.	Incorporated by reference to Exhibit 10.2 to the Quarterly Report on Form 10-Q, filed on October 25, 2005.
10.8	Employment Agreement effective as of September 1, 2009 between Mediware Information Systems, Inc. and Alan Wittmer.	Incorporated by reference to Exhibit 10.15 to the Annual Report on Form 10-K, filed on September 9, 2009.
10.11	Employment Agreement dated May 7, 2010 between Mediware Information Systems, Inc. and Thomas K. Mann.	Incorporated by reference to Exhibit 10.1 to the Current Report on Form 8-K, filed on May 13, 2010.
10.12	Employment Agreement dated May 7, 2010 between Mediware Information Systems, Inc. and John M. Damgaard.	Incorporated by reference to Exhibit 10.2 to the Current Report on Form 8-K, filed on May 13, 2010.
10.13	Employment Agreement dated May 7, 2010 between Mediware Information Systems, Inc. and Robert C. Weber.	Incorporated by reference to Exhibit 10.3 to the Current Report on Form 8-K, filed on May 13, 2010.
10.14	Mediware Information Systems, Inc. 2011 Equity Incentive Plan.	Incorporated by reference to Exhibit 10.1 to Current Report on Form 8-K, filed December 2, 2011.
10.15	Form of Mediware Information Systems, Inc. 2011 Equity Incentive Plan Non-Qualified Stock Option Award Agreement.	Incorporated by reference to Exhibit 10.2 to Current Report on Form 8-K, filed December 2, 2011.
10.16	Form of Mediware Information Systems, Inc. 2011 Equity Incentive Plan Restricted Stock Unit Award Agreement.	Incorporated by reference to Exhibit 10.4 to Current Report on Form 8-K, filed December 2, 2011.
10.17	Form of Mediware Information Systems, Inc. 2011 Equity Incentive Plan Restricted Stock Unit Award Agreement.	Incorporated by reference to Exhibit 10.4 to Current Report on Form 8-K, filed December 2, 2011.
10.18	Employment Agreement, dated as of February 15, 2012, between Mediware Information Systems, Inc. and Robert Watkins.	Incorporated by reference to Exhibit 10.5 to the Quarter Report on Form 10-Q, filed on February 7, 2012.

10.191	Amendment dated as of August 30, 2012 to the Employment Agreement made effective as of May 7, 2010 between Mediware Information Systems, Inc. and Thomas K. Mann.
10.201	Amendment dated as of August 30, 2012 to the Restricted Stock Agreement made as of May 1, 2010, by and between Mediware Information Systems, Inc. and Thomas K. Mann.
10.211	Amendment dated as of August 30, 2012 to the Employment Agreement entered into on May 7, 2010, and made effective as of June 1, 2010 between Mediware Information Systems, Inc. and John M. Damgaard.
10.221	Amendment dated as of August 30, 2012 to the Restricted Stock Agreement made as of May 7, 2010, by and between Mediware Information Systems, Inc. and John M. Damgaard.
10.231	Amendment dated as of August 30, 2012 to the Employment Agreement entered into on May 7, 2010 and made effective as of May 1, 2010 between Mediware Information Systems, Inc. and Robert C. Weber.
10.241	Amendment dated as of August 30, 2012 to the Restricted Stock Agreement made as of May 1, 2010, by and between Mediware Information Systems, Inc. and Robert C. Weber.
10.251	Amendment dated as of August 30, 2012 to the Employment Agreement made effective as of February 2, 2012 between Mediware Information Systems, Inc. and Robert Watkins.
10.261	Amendment dated August 30, 2012 to the Performance-Based Non-Qualified Stock Option Award Agreement dated February 2, 2012, by and between Mediware Information Systems, Inc. and Robert Watkins.
10.271	Amendment dated as of August 30, 2012 to the Employment Agreement made effective as of February 2, 2012 between Mediware Information Systems, Inc. and Alan Wittmer.
111	Mediware Information Systems, Inc. and Subsidiaries Computation of Net Earnings Per Share.
211	List of Subsidiaries.
231	Consent of EisnerAmper LLP.
31.11	Rule 13a-14(a)/15d-14(a) Certification.
31.21	Rule 13a-14(a)/15d-14(a) Certification.
32.11	Section 1350 Certification.
32.21	Section 1350 Certification.
1012	XBRL Instance
1012	XBRL Taxonomy Extension Schema
1012	XBRL Taxonomy Extension Calculation
1012	XBRL Taxonomy Extension Definition
1012	XBRL Taxonomy Extension Labels
1012	XBRL Taxonomy Extension Presentation

1.	Previously filed.

XBRL Information is furnished and not filed or a part of a registration statement or prospectus for purposes of sections 11 or 12 of the Securities Act of 1933, as amended, is deemed not filed for purposes of section 18 of the Securities Exchange Act of 1934, as amended, and otherwise is not subject to liability under these section.

SIGNATURES

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.

Date: September 24, 2012	MEDIWARE INFORMATION SYSTEMS, INC.


	By:	/s/ T. KELLY MANN
		T. KELLY MANN
		President and Chief Executive Officer

MEDIWARE INFORMATION SYSTEMS INC 10-K/A