Abstract: Objective To evaluate the clineffects of autologous and allogeneic hematopoietic stem cell transplantation (HSCT) for chronic myelogenous leukemia (CML).Methods Fifty-seven patients with CML were treated by HSCT, including 8 patients treated with autologous transplantation in vivo and vitro purging minimal residual disease (MRD), 39 with related donor allogeneic HSCT (allo-HSCT), and 10 with unrelated donor allo-HSCT. For the conditioning regimen, total-body irradiation with cyclophosphamide (CTX) was given in 32 patients, modified BuCY protocol (hydroxyurea, busulfan, Ara-C, CTX) in 24 patients, and MACC protocol (melphalan, Ara-C, CTX and lomustine) in one patient. Cyclosporine (CsA) and methotrexate (MTX) were used in patients with related donor allo-HSCT, and the combination of CsA, MTX, mycophenolate mofetil (MMF), and antithymocyte globulin (ATG) in unrelated donor all-HSCT to prevent graft versus host disease (GVHD). Kaplan-Meier survival analysis model was used to estimate the overall survival and the disease-free survival (DFS) at 5 years after transplantation.Results In 8 patients with autologous transplantation, 7 obtained partial or complete cytogenetic remission (CR) within 3 months after transplantation and one died of transplantation-related complication. In 49 patients with allo-HSCT transplantation, all patients obtained CR except for two patients, one of whom failed to obtain CR and the other died of hepatic veno-occlusive disease. The incidence of infection and veno-occlusive disease during transplantation was 33.3% and 7.0%, respectively. The incidence of hemorrhagic cystitis and cytomegalovirus interstitial pneumonia after transplantation was 22.8% and 8.8%, respectively. Veno-occlusive disease, hemorrhagic cystitis or cytomegalovirus interstitial pneumonia did not occur in patients with autologous transplantation. The incidence of acute GVHD was 41.0% and 48.6%, and that of chronic GVHD 40.0% and 42.9% in patients with related and unrelated transplantation, respectively. The rate of relapse was 57.1% and 12.8%, with DFS at 5 years of 25.0% and 61.7%, respectively, in patients with autologous and related donor transplantation. The DFS at 5 years was 70.7% and 34.1%, respectively, in patients with chronic/accelerated phases and blast crisis be fore trans plantation.Conclusion allo-HSCT can produce a higher clinical cure rate in CML patients in chronic phase CsA+MTX+MMF+ ATG protocol is more effective for prevention and alleviation of acute GVHD in patients with unrelated donor transplantation. Autologous transplantation with bone marrow purging helps prolong the patients’ survival and even obtain clinical cure of CML.