During Dr. Winkenwerder’s service there were significant advances in battlefield medicine, expanded mental health programs, and new benefits designated for U.S National Guard units and reservists. He led the global implementation of the Armed Forces Health Longitudinal Technology Application(AHLTA), a highly controversial and near-universally criticized electronic medical record system. Dr Winkenwerder's refusal to use an already established and well-regarded electronic medical system, such as the VistA system used by the Veterans Administration facilities, resulted in the implementation of a highly inferior product at an estimated total cost of $20 billion (four times the initial budget estimate). He also steered the critical cost-effective consolidation of Walter Reed Army Hospital and Bethesda Naval Hospital in Washington, DC.