Middlebrook Pharmaceuticals (MBRK) 10-Q 2007 Q3 Quarterly report

Exhibit 32.1

Certification of Principal Executive Officer
Pursuant to 18 U.S.C. 1350
(Section 906 of the Sarbanes-Oxley Act of 2002)

I, Edward M. Rudnic, Ph.D., President and Chief Executive Officer (principal executive officer) of MiddleBrook Pharmaceuticals, Inc. (the “Registrant”), certify, to the best of my knowledge, based upon a review of the Quarterly Report onForm 10-Q for the period ended September 30, 2007 of the Registrant (the “Report”), that:

(1) The Report fully complies with the requirements of Section 13(a) of the Securities Exchange Act of 1934, as amended; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Registrant.

/s/  EDWARD M. RUDNIC

Name:     Edward M. Rudnic, Ph.D.

Title:  President and Chief Executive Officer

Date: November 14, 2007