Body composition is sparsely described in spinal muscular atrophy (SMA). Body (BMI, mass/height in m(2)), fat-free (FFMI, lean mass/height in m(2)) and fat (FMI, fat mass/height in m(2)) mass indexes were estimated in 25 children (aged 5-18) with SMA (2 type I, 13 type II, 10 type III) using dual-energy radiograph absorptiometry and anthropometric data referenced to gender and age-matched healthy children (NHANES III, New York Pediatric Rosetta Body Project). BMI was 50th percentile in 11 (44%) and 85th in 5 (20%). FFMI was reduced (p<0.005) and FMI was increased (p<0.005) in the overall study cohort. FMI was 50th, 85th and 95th percentiles in 19 (76%), 10 (40%) and 5 (20%) subjects, respectively. Using a receiver operator characteristic curve, BMI above 75th, 50th and 3rd percentiles maximized sensitivity and specificity for FMI 95th, 85th and 50th percentiles, respectively. Children with SMA have reduced lean and increased fat mass compared to healthy children. Obesity is a potentially important modifiable source of morbidity in SMA.