Medicare Education Payment Clarification Act of 2003

Amends title XVIII (Medicare) of the Social Security Act with respect to the counting of residents in approved allopathic and osteopathic medical residency training programs for purposes of indirect medical education and direct graduate medical education payments. Requires the Secretary of Health and Human Services to reimburse teaching hospitals for residents in nonprovider settings, when the hospital incurs all, or substantially all, the costs of training in that setting, starting from the effective date of a written agreement between the hospital and the entity owning or operating the nonprovider setting. Requires the effective date to be determined in accordance with generally accepted accounting principles. Defines all, or substantially all, of the costs for the training program in that setting as the residents' stipends and benefits and other costs, if any, as determined by the parties.