Animal Drug User Fee Act of 2003

Animal Drug User Fee Act of 2003 - (Sec. 3) Amends the Federal Food, Drug, and Cosmetic Act to direct the Secretary of Health and Human Services to assess and collect fees for an animal drug application, defined as a request for approval of a new animal drug (not including generic drugs). Directs the Secretary to also assess fees for a supplemental animal drug application, defined as a request for a change in an approved animal drug application or in an approved generic animal drug application (if it requires safety or effectiveness data). Requires payment upon submission or the application will be considered incomplete and not accepted. Excepts from payment applications which were previously filed but withdrawn or not approved without a waiver or refund.

Assesses annual fees on animal drug products, establishments, and sponsors. Declares that only one such fee per category must be paid each year.

Establishes a fee schedule for FY 2004 through 2008, including total fee revenues for animal drug products, establishments, and sponsors. Adjusts fees to reflect inflation, review workload, and operating reserves of carryover user fees (in the final year).

Directs the Secretary to establish before each fiscal year, based on the fee schedule revenue amounts and the adjustments, the following: (1) animal drug application fees and supplemental animal drug application fees (for applications in which safety or effectiveness data are required); (2) animal drug sponsor fees; (3) animal drug establishment fees; and (4) animal drug product fees. Reduces or waives fees: (1) in excess of administrative costs; (2) that present a significant barrier to innovation; (3) if an animal drug application or supplemental animal drug application is intended solely for use of an animal drug in specified types of feed; (4) if an animal drug application or supplemental animal drug application is intended solely to provide for minor uses or use in minor species; or (5) for first applications by a small business.

Makes fees available for obligation only to the extent provided in advance in appropriations Acts.

Authorizes appropriations. Offsets any excess fees against subsequent appropriations.

(Sec. 4) Establishes public accountability and reporting requirements.

(Sec. 5) Establishes a sunset date of October 1, 2008, for the provisions of this Act not pertaining to public accountability and reports and a sunset date of 120 days after such date for such accountability and reporting provisions.