We describe the use of peripheral Quantitative Computed Tomography (pQCT) to identify musculoskeletal responses to partial body-weight supported treadmill training (BWSTT) in incomplete Spinal Cord Injury (SCI). Long-term health consequences of SCI include extensive muscle atrophy, severe bone loss and an increased fracture risk in the affected limbs, mostly at both tibial epiphyses and the distal femoral epiphysis. Regular treadmill training may slow or reverse bone loss by recruiting available lower-limb musculature and loading the leg bones dynamically. The potential for detailed analysis of musculoskeletal changes using pQCT is illustrated with a single case study (14.5 years post-SCI), who completed seven months of partial BWSTT. Pre- and post-training lower-limb pQCT scans were taken to quantify changes in trabecular bone, cortical bone, and soft-tissue. Trabecular bone mineral density increased by 5% (right) and 20% (left) in the distal tibia. Changes in proximal tibia and distal femur were negligible. Increases in muscle cross-sectional area were 6% (right) and 12% (left) in the lower leg, 7% (right) and 5% (left) in the thigh. We suggest that treadmill training may lead to positive musculoskeletal adaptations at clinically-relevant sites. Such changes can be measured in detail using pQCT.