Many patients with chronic myeloid leukemia (CML) retain a certain degree of normal hematopoiesis at disease presentation. This fact, suspected on the basis of cytogenetic findings, has been confirmed by long-term bone marrow cultures (LTBMC) and the combined use of phenotypic and molecular studies. Based on the lack of HLA-DR expression, it has been possible to recognize a benign subpopulation within the stem-cell compartment in CML. Different in vitro techniques have been developed for the selection of these benign progenitors, including LTBMC, marrow incubation with cytolytic drugs or interferon, positive selection based on their phenotypic characteristics, and exposure to synthetic antisense oligodeoxynucleotides. In vivo selection with interferon or intensive chemotherapy is also possible. The primary goal of the selection of benign hematopoietic progenitors is their use for autotransplantation. To date, a few hundred CML patients have been submitted to the latter procedure using bone marrow or peripheral blood. The fact that the majority of them show evidence of persistent disease emphasizes the necessity for better selection methods of the benign progenitors, for intensifying the conditioning regimen to reduce the tumor burden as much as possible, and for the use of adjuvant therapy post-transplantation. Future trends include the refinement of positive selection methods, negative selection by taking advantage of the different stromal adhesiveness of the benign and malignant progenitors, or the use of autologous natural killer cells, antisense oligodeoxynucleotides, or specific antibodies to the bcr/abl junction region, and retroviral marking to determine the origin of relapse in autologous transplantation.