This study sought to determine the association between BsmI polymorphism and bone mineral density, 25-hydroxyvitamin D, and parathyroid hormone levels in patients with epilepsy. We recruited ambulatory young adults with epilepsy who were taking phenytoin. Data regarding demographics, basic laboratory studies, history of clinical epilepsy, parathyroid hormone, and vitamin D levels, as well as BsmI polymorphism of the vitamin D receptor (VDR) gene, were obtained. The bone mineral density (BMD) of the lumbar spine and left femur were measured using dual-energy x-ray absorptiometry. Ninety-four patients were included in the study. BsmI polymorphism had a statistically significant lower T-score of the lumbar spine and left femoral neck than patients with wild-type VDR gene (p < 0.01 and p < 0.01, respectively). In addition, patients with BsmI polymorphism had a statistically significant lower z-score of the lumbar spine and left femoral neck than patients with wild-type VDR gene (p < 0.01 and p < 0.01, respectively). The 25-hydroxyvitamin D level in patients with wild-type genes was higher than in epileptic patients with BsmI polymorphism (p < 0.01 and p < 0.01, respectively). Parathyroid hormone level in patients with wild-type VDR gene or patients having BsmI polymorphism was not correlated with BMD at either site. In patients with epilepsy taking phenytoin, having BsmI polymorphism was associated with lower BMD.