To compare body composition in children with Prader-Willi syndrome (PWS) not naïve to growth hormone (GH) with obese and lean controls.Participants included 12 children with PWS, 12 children with obesity (body fat percentage >95th percentile for age and sex) and 12 lean children (body fat percentage <85th percentile for age and sex) matched by age and height. Fat mass, lean mass, bone mineral content (BMC), bone mineral density (BMD) and BMD z-score for total body, hips and lumbar spine were obtained through dual X-ray absorptiometry.PWS had higher fat percentage in the legs (p = 0.04) but similar leg fat mass (p = 1.00) compared to obese. PWS exhibited lower lean mass in the body (p = 0.04) and legs (p = 0.02) than obese, but similar to lean (p = 1.00 and p = 0.89, respectively). PWS had lower hip BMC (p < 0.01), BMD (p < 0.01) and BMD z-score (p < 0.01) compared to obese but similar to lean. No other differences were found between PWS and obese (p > 0.05 for all).Children with PWS not naïve to GH present differences in fat and lean mass distribution compared to obese controls. BMC and BMD appear unaffected by PWS, except at the hips.