The state of bone health and the effect of growth hormone (GH) therapy on bone and body composition in children with idiopathic short stature (ISS) are largely unknown. A direct role of GH deficiency (GHD) on bone density is controversial. Using dual-energy X-ray absorptiometry, this study measured total body bone mineral content (TB BMC), body composition, and volumetric bone mineral density (vBMD) at the lumbar spine (LS) and femoral neck (FN) in 77 children (aged 3-17 years) with ISS (n = 57) and GHD (n = 20). Fifty-five children (GHD = 13) receiving GH were followed over 24 months including measurement of bone turnover. At diagnosis, size-corrected TB BMC SDS was greater (P <or= 0.002) and LSvBMD SDS lower (P < 0.03) than zero in both prepubertal ISS and GHD subjects, but FNvBMD SDS was reduced only in the GHD group (P < 0.05). The muscle-bone relation, as assessed by the BMC/lean mass (LTM) ratio SDS was not different between groups. During GH therapy, prepubertal GHD children gained more height (1.58 [0.9] SDS) and LTM (0.87 [0.63] SDS) compared to prepubertal ISS children (0.75 [0.27] and 0.17 [0.25] SDS, respectively). Percent body fat decreased in GHD (-5.94% [4.29]) but not in ISS children. Total body BMC accrual was less than predicted in all groups accompanied by an increase in bone turnover. Puberty led to the greatest absolute, but not relative, increments in weight, LTM, BMI, bone mass, and LSvBMD. Our results show that children with ISS and GHD differ in their response to GH therapy in anthropometry, body composition, and bone measures. Despite low vBMD values at diagnosis in both prepubertal groups, size-corrected regional or TB bone data were generally within the normal range and did not increase during GH therapy in GHD or ISS children. Growth hormone had great effects on the growth plate and body composition with subsequent gains in height, LTM, bone turnover, and bone mass accrual, but no benefit for volumetric bone density over 2 years.