Background: Quantification of body composition variables is important for planning of better activities in relation to individuals with spinal cord injury (SCI). Objectives: (1) To evaluate changes in body composition in patients with SCI after a supervised physical activity process; (2) To correlate total body fat with time since injury. Design: Pre-post intervention. Setting: Sarah Rehabilitation Hospital Network, Brazil. Participants: Fifty-three men with SCI aged 18-52 years with duration of injury >3 years. Interventions: The subjects were divided into three groups: tetraplegia (TT) (C5-C8), high paraplegia (HP) (T1-T6), and low paraplegia (LP) (T7-L2). Body composition was estimated in the first and last weeks of hospitalization. Outcome measures: Body weight (kg), skinfolds sum (mm), absolute (kg), and relative (%) fat and lean body mass. Results: Body weight increased in TT and decreased in HP (0.8 kg, 95%CI 0.1-1.5; and −1.0 kg, 95%CI −2.0 to 0.0, respectively; P < 0.05). Skinfolds sum decreased only in HP (−13.1 mm, 95%CI −20.7 to −5.5; P < 0.05). Absolute and relative body fat decreased significantly in the paraplegia groups. Lean body mass (LBM) percentage increased significantly in the paraplegia groups. Absolute LBM increased in TT and LP (0.8 kg, 95%CI 0.3-1.3; and 1.3 kg, 95%CI 0.8 to 1.8, respectively; P < 0.05). There was no correlation between time since injury and skinfolds sum for the three groups (P < 0.05). Conclusion: TT, HP, and LP demonstrated favorable changes in body composition after 29 days of supervised physical activity. However, these changes were different in direction and magnitude.