We studied bone mineral density (BMD) in 79 long-term survivors of allogeneic stem cell transplantation (SCT) (median follow-up: 78 months; range: 38-160). Seventy patients received a total body irradiation (TBI)-based myeloablative SCT and 9 patients received a non-TBI, reduced-intensity SCT. Fourteen (18%) patients were receiving immunosuppressive therapy (IST) for chronic graft-versus-host disease (cGVHD) beyond 3 years from SCT. Fifty-eight (73.4%) of patients had bone loss (BL): 33 (41.8%) with osteopenia and 25 (31.6%) with osteoporosis. Factors associated with a significantly increased risk of osteoporosis were age and prolonged IST and for overall BL prolonged IST. However, BL was not associated with an increased fracture risk, despite the fact that most patients had not received prophylactic biphosphonates. Our data shows that BL is a long-term posttransplant complication, and emphasize the importance of serial BMD scans, and the treatment of BL with biphosphonates reserved for worsening BL or additional risk factors.