The purpose of this study was to evaluate the effects of ibandronate on bone loss following allogeneic stem cell transplantation (allo-SCT). A single-centered, open-label prospective randomized-controlled study following allo-SCT. The treatment group received 3 mg of intravenous ibandronate quarterly starting within 45 days of allo-SCT. All patients received daily calcium and vitamin D supplements. We compared the changes in bone mineral density (BMD) in the lumbar spine, femoral neck and total hip at 6 and 12 months following allo-SCT between the control and treatment groups. We also assessed relationships between bone loss and cumulative glucocorticoid dose, cumulative tacrolimus dose and acute and chronic graft-versus-host disease (GVHD) by linear regression. In all, 78 patients were enrolled. The treatment group had significantly less BMD loss in the lumbar spine at 6 months (mean percent change 0.06±4.03 (treatment group) versus À 2.61 ± 4.2 (control group)) and 12 months (mean percent change 1.27 ± 5.29 (treatment group) versus À 1.81±4.49 (control group)) than the control group (P ¼ 0.03). Both groups lost more BMD in the femoral neck and total hip than in the lumbar spine at 6 and 12 months. The changes in BMD in the femoral neck and total hip did not differ significantly between groups. Both glucocorticoids and tacrolimus reduced BMD in the lumbar spine, but ibandronate prevented this loss. Ibandronate may reduce bone loss in the lumbar spine in patients who undergo allo-SCT, particularly those who have received high doses of glucocorticoids and/or tacrolimus.