Childhood studies of the fat-bone relationship are conflicting, possibly reflecting the influence of metabolic abnormalities in some but not all obese children. Bone mass was compared between prepubertal overweight children with (n = 41) and without (n = 99) prediabetes. Associations of bone mass with measures of total and central adiposity, glucose intolerance, insulin sensitivity, lipid profile, systemic inflammation, and osteocalcin also were determined. In 140 overweight children aged 7 to 11 years, an oral glucose tolerance test was used to identify those with prediabetes and for determination of glucose, 2-hour glucose, glucose area under the curve (AUC), insulin, 2-hour insulin, and insulin AUC. Blood samples also were assessed for lipids, C-reactive protein, and osteocalcin. Total-body bone mineral content (BMC), fat-free soft tissue mass (FFST), and fat mass (FM) were measured by dual-energy X-ray absorptiometry (DXA). Visceral adipose tissue (VAT) and subcutaneous abdominal adipose tissue (SAAT) were assessed using MRI. Total-body BMC was 4% lower in overweight children with prediabetes than in those without prediabetes after controlling for sex, race, height, and weight (p = .03). In the total sample, FM was positively related with BMC (β = 0.16, p = .01) after adjusting for sex, race, height, and FFST. However, VAT (β = -0.13, p = .03) and SAAT (β = -0.34, p = .02) were inversely associated with BMC after controlling for sex, race, height, FFST, FM, and SAAT or VAT. No significant associations were found between BMC and the biochemical measurements. Prepubertal overweight children with prediabetes may be at risk for poor skeletal development. In addition, it appears that greater levels of central rather than total adiposity may be deleterious for developing bone.