The overall focus of this thesis was musculoskeletal changes after individuals with spinal cord injury. The bulk of the thesis investigated the impact of a rehabilitation intervention, namely body weight supported treadmill training (BWSTT), on skeletal health and muscle atrophy in individuals with acute and chronic spinal cord injury (SCI). The first two studies in this thesis were methodological in nature. The first revealed that the presence of metal in a dual-energy x-ray absorptiometry scan results in reproducible errors in estimations of bone mineral content and body composition. The second study demonstrated that mid-tibia speed of sound measurements obtained with quantitative ultrasound might not reveal the changes that occur in the skeleton after SCI. These studies impart an important contribution to the area of osteoporosis diagnosis in individuals with SCI. The two longitudinal prospective studies presented here add to the growing body of literature that BWSTT can improve ambulation in individuals with chronic and acute incomplete SCI. Individuals participating in regular BWSTT improved their walking abilities on the treadmill, and some individuals improved their over ground walking abilities. The studies in this thesis are the first to investigate the impact of BWSTT on bone and muscle together in individuals with acute and chronic SCI. BWSTT had a positive impact on muscle, in that significant increases in lean mass and muscle cross-sectional area were observed after training in both acute and chronic SCI. BWSTT did not appear to have an impact on the skeleton, but further research is required to confirm these findings. Ultimately, it appears that individuals with SCI stand to benefit from BWSTT and the benefits are not limited to improved ambulation.