Animal Drug User Fee Act of 2003

Animal Drug User Fee Act of 2003 - 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 or a supplemental 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 Excepts from payment applications which were previously filed but withdrawn or not approved without a waiver or refund.Assesses annual fees on animal drug products, establishments, and sponsors.Establishes a fee schedule for FY 2004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; (2) supplemental 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. Offsets any excess fees against subsequent appropriations.