Hematopoietic stem-cell transplantation (HCT) and organ transplantation have become the standard of care for a number of malignant and non-malignant disorders. Neurological complications associated with these procedures remain frequent. These complications result from a variety of causes including the underlying disorder, therapies used for immunosuppression, and toxicities from radiation or chemotherapy. For HCT the frequency of some complications is dependent on whether the transplant is allogenic or autologous. In general, the main neurological problems of HCT and organ transplantation include metabolic and toxic encephalopathies, and central and peripheral neurological disorders caused by coagulopathy, infections, and autoimmune mechanisms. The term post-transplant lymphoproliferative disorder (PTLD) includes a spectrum of disorders ranging from benign polyclonal lymphoid hyperplasia to malignant monoclonal lymphoma, usually related to the Epstein-Barr virus. Some lesser known syndromes such as the immune reconstitution inflammatory syndrome and paraneoplastic neuropathies related with PTLD are increasingly being described and need to be considered in the evaluation of a transplant patient with neurological problems.