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Hematopoietic cell transplantation (HCT) is widely performed for neoplastic and non-neoplastic diseases.HCT involves intravenous infusion of hematopoietic progenitor cells from human leukocyte antigen (HLA)-matched donor (allogeneic) or from the patient (autologous).Before HCT,the patient is prepared with high dose chemotherapy and/or radiotherapy to destroy residual malignant cells and to reduce immunologic resistance.After HCT,chemotherapy is used to prevent graft rejection and graft versus host disease (GvHD).Neurological complications are related to the type of HCT,underlying disease,toxicity of the conditioning regimens,immunosuppression caused by conditioning regimens,vascular complications generated by thrombocytopenia and/or coagulopathy,GvHD and inappropriate immune response.In this review,neurological complications are presented according to time of onset after HCT:(1) early complications (in the first month)-related to harvesting of stem cells,during conditioning (drug toxicity,posterior reversible encephalopathy syndrome),related to pancytopenia,(2) intermediate phase complications (second to sixth month)-central nervous system infections caused by prolonged neutropenia and progressive multifocal leukoencephalopathy due to JC virus,(3) late phase complications (after sixth month)-neurological complications of GvHD,second neoplasms and relapses of the original disease.