Bone marrow transplantation offers a potential cure for a number of childhood cancers, sickle cell anemia, and stabilization of a deteriorating and debilitating process in a number of metabolic disorders and leukodystrophies. Depending upon the disease, treatment prior to BMT, and natural history of the disease, BMT may increase the risk of neuropsychological toxicity for children undergoing BMT, or may actually improve their long-term neurodevelopmental outlook. The role of factors such as pre-BMT therapy, age at time of treatment, presence or absence of total body irradiation, and toxicities associated with GVHD are presented for consideration. A developmental model for understanding the emergence of neurocognitive effects of BMT is reviewed, and strategies for intervention are considered.