Since decades myeloablation followed by allogeneic stem cell transplantation offered the only opportunity to cure leukemia patients and only recently the development of STI571 created a further alternative in chronic myeloid leukemia (CML). While among all leukemias this transplantation regimen had the best outcome in CML, trials with reduced intensity conditioning regimens (RIC) were rather humbling and recurrence of the neoplastic clone occurred frequently. However, the same therapy in patients with idiopathic myelofibrosis (IMF) resulted in a more favorable outcome. Therefore, long-term mixed chimerism (mCh) was determined on bone marrow (BM) biopsies derived from five IMF patients and from eight CML patients of the pre STI era following sex-mismatched transplantation. All patients presented lasting hematologic remission and were matched concerning age, sex and appearance of GvHD. Analysis of late transplant period (day +100) revealed a concentration of host cells within the CD34+ precursor cell compartment in both diseases. However, in IMF BM biopsies only up to 8% recipient CD34+ precursors but in CML biopsies up to 26% recipient CD34+ precursors were detected. Taken into account that in CML up to 10% of the host BM CD34+ precursors bear the BCR-ABL translocation our data suggest that the neoplastic CD34+ progenitor cell population might dispose of better strategies to escape immune surveillance in CML than in IMF.