Transplantation of bone marrow or peripheral blood stem cells is increasingly being used to treat a variety of oncologic disorders. These procedures are associated with a large spectrum of neurologic complications that significantly contribute to patient morbidity and mortality. These complications may arise at any time during and after the transplantation process and are particularly common in patients requiring chronic immunosuppression. The most frequent complications are infections and cerebrovascular or metabolic events, and toxicity from radiation or chemotherapy. Because of the unique circumstances and treatments involved in each step of the transplantation process, there is a higher incidence of some neurologic complications during discrete time periods, and an awareness of the temporal relationship of the neurologic disorder to the transplantation process facilitates diagnosis. With the exception of post-transplant lymphoproliferative disorder, in which reduced immunosuppression may be an effective therapeutic strategy, therapies are often the same as in the nontransplant patient. Complications of therapy can arise because of the presence of multiple comorbidities and medication interactions. Anticipation of common opportunistic infections and appropriate use of prophylactic medications can significantly reduce the incidence of infectious complications.