This paper presents a running control architecture for a powered knee and ankle prosthesis that enables a transfemoral amputee to run with a biomechanically appropriate running gait and to intentionally transition between a walking and running gait. The control architecture consists firstly of a coordination level controller, which provides gait biomechanics representative of healthy running, and secondly of a gait selection controller that enables the user to intentionally transition between a running and walking gait. The running control architecturewas implemented on a transfemoral prosthesis with powered knee and ankle joints, and the efficacy of the controller was assessed in a series of running trials with a transfemoral amputee subject. Specifically, treadmill trials were conducted to assess the extent to which the coordination controller provided a biomechanically appropriate running gait. Separate trials were conducted to assess the ability of the user to consistently and reliably transition between walking and running gaits.