The objective of this study was to identify how many children with hypercalciuria and/or nephrolithiasis have a low bone density and whether the risk of low bone density can be identified by 24-h urine stone-risk profiles and/or growth parameters. A retrospective chart review was performed on 110 idiopathic hypercalciuria and/or kidney stone patients who received both a 24-h urine for stone-risk profile and a dual-energy X-ray densitometry scan. Patients were divided into low bone density vs. normal bone density groups and hypercalcuria verus nephrolithiasis groups and analyzed for differences in growth parameters, urine stone-risk profiles, and bone densities. Overall, 47% had a bone density z score < -1, and 26% had a bone density z score < -2. Patients with a low bone density had a higher body mass index and lower urine creatinine and ammonium than those with a normal bone density. Patients with nephrolithiasis had a lower bone density z score than patients with hypercalcuria and no nephrolithiasis. Clinicians should be aware of the increased incidence of low bone density in children with hypercalciuria and nephrolithiasis. The effect of hypercalciuria and nephrolithiasis treatment on bone density and the natural progression of the bone density in the studied patient population warrants further investigation.