Bone density is related to body size and other factors including dietary calcium intake. The purpose of this study was to determine the effect of a low-lactose, low-calcium diet on the bone mineral content (BMC) of prepubertal children with documented lactose intolerance. Radial BMC was determined by single-photon absorptiometry. Dietary intake was assessed by 24-h recall and two 3-day food records, and weight and height were measured. The group of lactose-intolerant children was compared with a group of healthy children of similar age, gender, race, and size and to the prediction equations based on body size from Chan's Utah children. Nineteen children, ages 9.6 +/- 1.9 years, participated in the study. They were relatively short compared with standards (height Z score, -0.30 +/- 0.83). BMC was 0.428 +/- 0.081 g/cm in the study group versus 0.440 +/- 0.116 g/cm in the comparison group (n = 19; p > 0.05). Both the study group and the size-selected comparison group had lower BMC than the Utah children. The diet of the study group was low in calcium: 84% of the Recommended Dietary Allowance in children < 11 years old and 32% in children > 11. Calcium intake was associated (p = 0.03) with BMC in the study group after adjusting for body size. The low-lactose diet resulted in a low calcium intake, and BMC was associated with calcium intake in prepubertal children with lactose intolerance. Evaluation of dietary calcium intake should be considered in this group of patients, with follow-up dietary counseling, calcium supplementation (diet or medication), and bone density assessment when clinically indicated.