The loss of bone mass often occurs after patients undergo bone marrow transplantation (BMT). The rapid impairment of bone formation and the increase in bone resorption, as mirrored by the biochemical markers of bone turnover, might play a role in this bone loss, and especially during the immediate post-BMT period. The possible direct causes for this paradoxical uncoupling are exposure to immunosuppressants, hypogonadism, the changes of cytokines, the changes of the bone growth factors, and the damage to the osteoprogenitor cells because of myeloablative therapy. In this chapter, we discuss the general aspects of post-BMT bone loss with a peculiar focus on the remodeling imbalance of bone and its relation to the use of immunosuppressants and the changes of sex hormones, growth factors, and cytokines.