Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is regarded as a curative option for aggressive adult T cell leukemia-lymphoma (ATL). However, the efficacy and safety of allo-HSCT for ATL with central nervous system (CNS) involvement, which is highly resistant to chemotherapy, remain controversial. We analyzed 10 ATL patients with CNS involvement who received allo-HSCT at three institutions in Nagasaki prefecture between 2000 and 2007. The 3-year overall survival rate was 40%, and the median observation time of the four surviving patients was 1532 days (range 945-2212 days). Two of four surviving patients received highly intensive local treatment for the CNS; one with 26 intrathecal injections of antineoplastic agents, and the other with whole cerebrospinal irradiation before transplantation. However, the other two patients received conventional or reduced-intensity conditioning with standard intrathecal chemotherapy. Three of the four surviving patients experienced chronic GVHD, and two of three patients with grade 3 or 4 acute GVHD were free from CNS relapse. From these data, it seems that both intensive local treatment for CNS disease and systemic GVHD contributed to the long-term control of CNS involvement. Although our data suggest that allo-HSCT is a therapeutic option for ATL with CNS disease, high transplant-related mortality (six cases) indicates the need for further studies to develop more effective procedures for CNS disease, and to reduce transplant-related morbidity.