To determine the effect of thiazide treatment on bone mineral density (BMD) in children with idiopathic hypercalciuria (IH) and osteopenia, we reviewed the case notes of 22 children aged 11.7 ± 2.7 years diagnosed with IH and osteopenia who had received thiazides for 2.4 years. The data on this group were compared with those of 32 IH children with osteopenia aged 11.2 ± 2.7 years who had not received thiazide treatment. By the end of the follow-up period, the z-BMD had improved spontaneously in 23 of the 32 control children (72%) and in 12 of the 22 patients on thiazides (54%). Although treated patients had a higher body mass index (BMI) and a higher BMD following treatment, the differences became statistically negligible when these parameters were expressed as z-BMD or as bone mineral apparent density (BMAD). In contrast, within the control group, there were significant differences in BMAD and z-BMD at the end of the follow-up. Patients who had an improved z-BMD at the end of the treatment also showed an increase in their BMI. Based on these results, we conclude that thiazide treatment does not improve the z-BMD in children with IH. More than half of the children suffering from IH enrolled in our study showed a spontaneous improvement in their z-BMD, which was more evident when the initial BMAD was not low and when their BMI increased during the follow-up period.