Allogeneic hematopoietic stem cell transplantation (allo-SCT) is one of the options for curative treatment of aplastic anemia. However, physicians often hesitate in selecting this option due to the lack of ample evidence regarding the optimal conditioning regimen and long-term outcomes of allo-SCT from alternative donors. Allo-SCT is the first choice of treatment in patients under 40 years of age with stage 3-5 aplastic anemia who possess HLA-matched sibling donors. Allo-SCT from alternative donors such as unrelated individuals or employing umbilical cord blood should be considered for patients with disease refractory to immunosuppressive therapy. High dose cyclophosphamide (CY) which was formerly used as the standard conditioning regimen is currently being replaced by a reduced dose CY regimen combined with fludarabine to avoid cardiotoxicity. Peripheral blood stem cell transplantation must be avoided due to the higher incidence of chronic GVHD than with bone marrow transplantation. Among transplants from alternative donors, HLA-haploidentical SCT from related donors using post-transplant CY is now attracting considerable attention due to its low transplant-related mortality and low incidence of chronic GVHD.