ABSTRACT: Spinal cord injury (SCI) is accompanied by deterioration in body composition and severe muscle atrophy. These changes put individuals at risk for insulin resistance, type II diabetes, and cardiovascular disease. To determine the relationships between skeletal muscle mitochondrial mass, activity, and body composition, 22 men with motor complete SCI were studied. Body composition assessment was performed using dual-energy X-ray absorptiometry and magnetic resonance imaging. Skeletal muscle biopsies were obtained from the vastus lateralis muscle to measure citrate synthase (CS) and complex III (CIII) activity. CS activity was inversely related to %body fat (r = -0.57, P = 0.013), %leg fat (r = -0.52, P = 0.027), %trunk fat (r = -0.54, P = 0.020), and %android fat (r = -0.54, P = 0.017). CIII activity was negatively related to %body fat (r = -0.58, P = 0.022) and %leg fat (r = -0.54, P = 0.037). Increased visceral adipose tissue was associated with decreased CS and CIII activity (r = -0.66, P = 0.004; r = -0.60, P = 0.022). Thigh intramuscular fat was also inversely related to both CS and CIII activity (r = -0.56, P = 0.026; r = -0.60, P = 0.024). Conversely, lean mass (r = 0.75, P = 0.0003; r = 0.65, P = 0.008) and thigh muscle cross-sectional area (CSA; r = 0.82, P = 0.0001; r = 0.84; P = 0.0001) were positively related to mitochondrial parameters. When normalized to thigh muscle CSA, many body composition measurements remained related to CS and CIII activity, suggesting that %fat and lean mass may predict mitochondrial mass and activity independent of muscle size. Finally, individuals with SCI over age 40 had decreased CS and CIII activity (P = 0.009; P = 0.004), suggesting a decrease in mitochondrial health with advanced age. Collectively, these findings suggest that an increase in adipose tissue and decrease in lean mass results in decreased skeletal muscle mitochondrial activity in individuals with chronic SCI.