Pharmaceutical Fiscal Accountability Act of 2003

Pharmaceutical Fiscal Accountability Act of 2003 - Amends the Federal Food, Drug, and Cosmetic Act to treat certain subsequent certified abbreviated new drug applications as if they were the first such application and therefore entitled to a period of 180 day generic drug exclusivity. (Abbreviated new drug applications are filed where the new drugs uses or active ingredient(s) are the same as those for a previously approved drug, also known as a "listed drug.")

Amends the Public Health Service Act to require the Director of the National Institutes of Health to support qualifying clinical research on the development of new drugs at designated small public or private entities. Emphasizes drug research which has the potential to make a significant contribution for the prevention, diagnosis, or treatment of a disease which has not received significant Federal funding. Entitles the Director to five percent of the profits from sales during the patent period.

Requires the Comptroller General to study and report to Congress on the effects of: (1) Federal funding on the costs of research and the pricing of prescription drugs; and (2) pharmaceutical patent extensions and market exclusivity periods on delays in introducing generic versions.