Spinal cord injury (SCI) induces dramatic changes in body composition including reductions in fat-free mass (FFM) and increases in fat mass (FM). Objective: To examine changes in body composition in response to chronic activity-based therapy (ABT) in persons with SCI. Design: Longitudinal exercise intervention. Methods: Seventeen men and women with SCI (mean age = 36.1 ± 11.5 years) completed 6 months of supervised ABT consisting of load bearing, resistance training, locomotor training, and functional electrical stimulation. At baseline and after 3 and 6 months of ABT, body weight, body fat, and FFM were assessed using dual-energy X-ray absorptiometry, and fasting blood samples were obtained to assess changes in insulin-like growth factor-I (IGF-I), adiponectin, and myostatin. Results: Across all subjects, there was no change (P > 0.05) in body weight, percent body fat, or FFM of the leg, arm, or trunk, whereas whole-body FFM declined (P = 0.02, 50.4 ± 8.4 to 49.2 ± 7.4 kg). No changes (P = 0.21-0.41) were demonstrated in IGF-I, adiponectin, or myostatin during the study. Conclusions: Chronic ABT focusing on the lower extremity does not slow muscle atrophy or alter body fat, body mass, or regional depots of FFM in persons with SCI. Further, it does not induce beneficial changes in adiponectin, myostatin, or IGF-I. Alternative exercise-based therapies are needed in SCI to reverse muscle atrophy and minimize the onset of related health risks.