The transplantation of hematopoietic stem cells (HSCT) is an established part of the therapy of hematologic neoplasia and certain solid tumors. In the allogeneic approach hematopoietic stem cells are harvested from healthy donors, while in the autologous setting preparations originating from the patient himself are being used. Both therapies use high dose cytotoxic medication for the induction of higher remission rates in malignant diseases. While autologous HSCT rescues hematopoiesis after high dose chemotherapy, in allogeneic HSCT donor immune cells exert an additional allo-reactivity towards recipient tissue and residual malignant cells. Autologous HSCT is mainly used in relapsed malignant high-grade lymphoma. Allogeneic HSCT results in cure from acute leukemia with unfavorable prognosis in a high percentage of patients. Recent developments target the expansion of the donor pool for allogeneic stem cells and want to reduce chemotherapeutic toxicity of allogeneic transplantation with sustained anti-leukemia efficacy.