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Caring and rehabilitation of spinal cord injuries have greatly evolved during the twentieth century. Unfortunately standard training still heavily relies on manual mobilization of the patient. Which not only results in short training periods, but also prevents the patient's muscles from contracting, if voluntary control is lost. In order to cope with these issues the Fondation Suisse pour les Cyberthèses (FSC) in collaboration with the Laboratoire de Systèmes Robotiques (LSRO) from EPFL initiated a three step reeducation project. The main idea is the combination of motorized orthoses and closed loop muscle stimulation in order to enable an active participation of the patient, with a smart muscle control. The three complementary projects are: MotionMaker: stationary device with hip, knee and ankle mobilization combined to muscle stimulation. WalkTrainer: mobile device for true overground deambulation, with leg and pelvis orthoses, active body weight support and muscle stimulation. WalkMaker: lightweight orthosis with muscle stimulation, for enhanced autonomy. This work focuses on the control of the WalkTrainer, both of the motors and the muscle stimulation. First optimal trajectory generation is discussed. For the pelvis a three step strategy is presented. That consists of measuring motions on valid subjects with different parameters, identifying the corresponding model that can then be incorporated in the trajectory generator of the WalkTrainer. Of course the same work could be undertaken for any motion, such as the ones applied to the legs or trunk. Second, a novel off line EMG based muscle model and closed loop stimulation algorithm were developed. The trajectory generation and the muscle stimulation were then combined to obtain a novel, third generation, rehabilitation strategy. That optimizes the afferent feedback of the subject, while allowing an active participation of his musculature. That strategy was successfully tested on 6 paraplegic subjects at the beginning of 2008.