Bone marrow transplantation (BMT) is widely performed for both neoplastic and non-neoplastic disease. Before BMT, patients are prepared with high-dose chemotherapy, frequently associated with total-body radiation, to destroy residual malignant cells and to reduce immunologic resistance. BMT is associated with several central nervous system (CNS) complications secondary to underlying disease, prolonged myelosuppression, and the use of immunosuppressive drugs. These complications include infections, vascular disease, drug-induced neurotoxicity, metabolic disturbance, and post-BMT carcinogenesis. The immune status of children after BMT can be divided into three phases: the pre-engraftment period (days 0-30 after BMT), the post-engraftment period (days 30-100), and the late phase (after day 100). The timing of CNS complications that occur after BMT, as for complications in other organs, can be described with reference to these three phases of immune status. It is essential that radiologists become familiar with the relationships between the immune status of the recipient and the times of onset of these disorders, and with the neuroimaging patterns associated with the various complications. CNS complications can be life-threatening for immunosuppressed children, so accurate diagnosis is important for prompt and appropriate treatment.