Despite reports of decreased bone density, children with mild to moderate cystic fibrosis (CF)-associated pulmonary disease do not have increased fracture rates. Short stature and delayed puberty complicate interpretations of bone mineral status in many children with chronic diseases. This study sought to characterize bone mineral content (BMC) in children with CF and determine its relationship to growth, body composition, and disease severity. Dual-energy X-ray absorptiometry measurements of whole body BMC (WB-BMC), spine BMC (Sp-BMC), and lean body mass (LBM) were converted to Z-scores in 82 CF and 322 healthy children. Effects of growth, body composition, and CF-disease characteristics on BMC were determined using linear regression. Children with CF had lower weight, height (HT), BMI, and LBM-Z. Females with CF had lower (p<0.001) WB-BMC-Z (-1.1+/-1.1) and Sp-BMC-Z (-0.9+/-1.1) than controls. Following adjustment for height standard deviation score (HT-Z), deficits were absent. Males with CF had lower (p<0.001) WB-BMC-Z (-1.3+/-0.9) and Sp-BMC-Z (-0.9+/-1.3). Following adjustment for HT-Z, WB-BMC-Z deficits were attenuated and Sp-BMC-Z deficits absent. HT-Z, LBM-Z, and pulmonary function had independent effects on WB-BMC-Z and Sp-BMC-Z. BMC deficits are related to altered body size, reduced LBM, and pulmonary function in children with CF. Interventions targeting improved growth, muscle mass, and pulmonary function may benefit bone health in CF.