Autologous bone marrow transplantation has become an established procedure in the treatment of malignancies. Especially in patients with hematological malignant diseases, who have no compatible allogeneic bone marrow donor or in patients with solid tumors, in whom the threshold of irreversible bone marrow toxicity is reached by the intensified chemotherapy, this procedure allows the use of a myeloablative therapy. As stem cell sources, bone marrow (BM), peripheral blood-derived stem cells (PBSC), and umbilical cord blood can be used. The risk of contaminating malignant cells in BM or PBSC can be reduced by an in vitro purging of the stem cells. In principle, two different methods exist: one is the negative depletion of contaminating tumor cells and the other is the positive selection of non-malignant hematopoietic pluripotent stem cells. Which of the purging principles will be most effective can only be answered through clinical studies.