Children with myelomeningocele experience difficulty with ambulation, which leads to immobilization and secondary loss of bone mineral density (BMD). In addition, non-ambulatory myelomeningocele patients have higher urinary calcium losses than their ambulatory counterparts. Hydrochlorothiazide (HCTZ) is known to reduce urinary calcium loss and increase BMD in non-myelomeningocele patients with hypercalciuria. This study examines the effect of HCTZ on urinary calcium and BMD in non-ambulatory children with myelomeningocele. Thirteen of 20 non-ambulatory patients with myelomeningocele completed the year-long randomized double-blinded study (placebo = 7 and HCTZ = 6). Evaluation included electrolytes, PTH, osteocalcin, 1, 25-OH vitamin D, urinary pyridinolines/deoxypyridinolines (Upyr/dpyr), urinary calcium/creatinine (UCa/Cr), and forearm BMD (dual X-ray absorptiometry). Follow-up electrolytes were obtained at 1–2, 6, and 12 months and UCa/Cr and BMD was obtained again at 12 months. There were no initial differences between the placebo and HCTZ groups. UCa/Cr decreased in the HCTZ group after treatment (0.20±0.09 vs. 0.04±0.02, p<0.05). However, forearm BMD (z-scores) after 1 year remained unchanged in both the HCTZ (−5.95±0.98 to −5.86±0.92) and placebo (−7.19±0.69 to −6.67±0.63) groups. While use of HCTZ for 1 year did not affect BMD, it reduced urinary calcium excretion in non-ambulatory children with myelomeningocele.