Bone marrow transplantation is now an established successful treatment for several hematologic malignancies. Bone loss is among the long-term adverse effects of this procedure. The underlying pathophysiology is believed to be multifactorial. We report a case of osteoporosis in a young patient who underwent allogenic bone marrow transplantation for acute lymphoblastic leukemia that was complicated by intestinal graft-versus-host disease. Her bone density measurement showed T-scores of −3.46 and −2.47 in the lumbar spine and femoral neck respectively. On evaluation, she had low normal serum calcium, low urine calcium, low 25-hydroxyvitamin D, elevated total and bone specific alkaline phosphatases, and elevated parathyroid hormone. Following treatment with calcifediol, the biochemical markers normalized and the bone mineral density increased by 88% in the lumbar spine and almost 60% in the femoral neck, both of which were above the mean for her age group. We believe that the graft-versus-host disease caused a malabsorptive state that led to vitamin D deficiency and possible resistance and consequent osteomalacia.