Medicare Physician Payment Equity Act of 2003 - Amends title XVIII (Medicare) of the Social Security Act to provide for: (1) establishment of a uniform national Medicare physician fee schedule; and (2) phase-out of geographic adjustment indices.Directs the Comptroller General to study and report to Congress on: (1) the recruitment and retention of physicians; (2) the access of Medicare beneficiaries to physicians, medical tests, and medical therapies in each fee schedule area; and (3) the use by Medicare beneficiaries of items and services for which payment may be made under the Medicare program in each such fee schedule area.