Currently, autologous hematopoietic stem cell (SCT) transplantation is frequently used as a method of treatment for various hematologic malignant neoplasms and some solid tumors in adults and children. Autologous stem cells can be obtained in most instances from the patient's bone marrow or peripheral blood. The blood is the preferred source of stem cells because of easier collection and faster hematologic recovery post-transplantation. Prospective clinical trials confirmed the role of autologous SCT in the treatment of chemosensitive non-Hodgkin's lymphomas and Hodgkin's disease after first relapse, and probably in selected high-risk patients in earlier stage of the disease. In multiple myeloma, autologous SCT is a standard treatment approach for all patients younger than 65, either as a single transplant or as a tandem transplant in patients that failed to achieve complete or very good response after first transplant. In acute leukemia, the role of autologous SCT is less well defined although in acute myeloid leukemia several studies resulted in statistically superior patient outcome in comparison to chemotherapy. Advances in supportive therapy and use of peripheral blood stem cells have made autologous SCT a relatively safe treatment modality with attributable mortality mainly less than 5%. Yet, the relatively high incidence of relapse after transplantation remains a major problem. A variety of methods have been under investigation before and after transplantation to reduce the risk of relapse and improve the results of treatment.