We have studied the differences between the peripheral and axial skeleton of pre-pubertal gymnasts and controls. We hypothesised that compared to controls, gymnasts would have larger and stronger radius and tibia diaphyses with greater bone mineral content and larger cross-sectional muscle area. At the distal metaphyseal sites of the radius and tibia, gymnasts would have greater bone cross-sectional area and total and trabecular volumetric bone mineral density (vBMD). Differences between the lumbar spine, total body and body composition in gymnasts versus controls were also studied. Peripheral quantitative computed tomography (pQCT) was used to measure bone geometry, density and muscle of the peripheral skeleton; dual energy X-ray absorptiometry (DXA) for total body and axial measurements. Eighty-six pre-pubertal children, 44 gymnasts (mean age 9.0 years, range 5.4-11.9 years) and 42 controls (mean age 8.8 years, range 5.6-11.9 years) were studied. Eighty-four children were Caucasian, one child was mixed race, one Chinese. Data were adjusted for age, sex and height. Differences in the effect size between sexes were also tested. At the 50% radius diaphysis gymnasts had larger bones (9.2%, p = 0.0054) with greater cortical area (8.2%, p = 0.022) and stress strain index (surrogate measure of bone strength) than controls (13.6%, p = 0.015). The effect size was different between males and females for cortical thickness (p = 0.03). At the 65% tibia diaphysis, gymnasts had greater cortical area (5.3%, p = 0.057) and thickness (6.2%, p = 0.068) than controls; consequently, bone strength was 5.4% higher (p = 0.14). There were no significant differences in cortical volumetric bone mineral density (vBMD) at the radius or tibia diaphysis between the groups. There was a difference in effect size for tibia muscle cross-sectional area between the sexes (p = 0.035). At the distal radius and tibia total and trabecular vBMD was greater (Total: radius 17%, p < 0.0001, tibia: 5.7%, p = 0.0053; trabecular: radius 21%, p < 0.0001, tibia 4.5%, p = 0.11). Bone size was not different in gymnasts compared to controls Lumbar spine BMC (12.3%, p = 0.0007), areal bone mineral density (aBMD) (9.1%, p = 0.0006) and bone mineral apparent density (BMAD) (7.6%, p = 0.0047) were greater in gymnasts but vertebral size was not significantly different. Likewise, total body BMD (3.5%, p = 0.0057) and BMC (4.78%, p = 0.085) were greater in gymnasts but there were no differences in skeletal size. These data suggest site-specific differences in how the pre-pubertal skeleton develops in response to the repetitive loading it experiences when participating in regular gymnastics. At diaphyseal sites these differences are predominantly in the bone and muscle geometry and not density. Conversely, at trabecular sites, the differences are increased density rather than geometry. In conclusion, the present study has demonstrated skeletal differences between gymnasts and controls. These differences appear to be site and sex specific.