Study design: Cross-sectional study comparing athletes with spinal cord injury (SCI) and age and body mass index matched able-bodied controls (AB). Objective: To examine the impact of exercise training on the relation between whole body, regional and intermuscular adipose tissue (IMAT) and glucose tolerance, insulin action and lipid profile. Setting: University Research Laboratory, USA. Methods: Fourteen college-aged athletes with SCI (seven men; duration of injury 16.575.7 years, level of injury T5-L5) and 17 sedentary AB (eight men) were assessed for body composition via dual-energy X-ray absorptiometry (DXA) and magnetic resonance imaging. Insulin sensitivity index (ISI) was determined via 2-h oral glucose challenge; standard lipid profile was determined from fasting blood samples. Results: Although ISI was 30% higher in SCI, there were no significant differences between groups in glucose and insulin responses or in lipid measures. Adjusting for absolute and relative thigh IMAT area, fasting insulin (13.875.3 mIU, 16.375.6 mIU; Po0.05; SCI vs AB respectively) and ISI (4.071.4, 3.171.3; Po0.05) were significantly better among SCI athletes compared to AB. Measures of adiposity did not correlate with glucose response or most lipid measures. Within SCI and AB, respectively, ISI correlated strongly (all Po0.05) with absolute (r ¼ À0.70, À0.54) and relative IMAT (r ¼ À0.54, À0.50), than with trunk (r ¼ À0.62, À0.64) and whole body fat mass (r ¼ À0.61, À0.64). Conclusion: Habitual physical activity can maintain insulin sensitivity in SCI compared to sedentary AB controls. Total body fat mass, central adiposity and thigh IMAT appear to impact risk for metabolic disease in SCI individuals with IMAT playing a larger role in SCI than AB.