BACKGROUND: Allogeneic hematopoietic stem cell transplantation is recognized as the only method of curing chronic myelocytic leukemia (CML). Lmatinib mesylate (STI571) is a competitive inhibitor of the bcr-abl tyrosine kinase, as a represent of synthetic gene-targeting drug in recently, which has been used more and more on the Philadelphia chromosome positive CML patients.OBJECTIVE: To compare the efficacy and safety of STI571 to related allogenic hematopoietic stem cell transplantation in the treatment of CML patients.DESIGN, TIME AND SETTING: A controlled observation between ST1571 treated group and transplantation group was performed in the Department of Hematology, Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology between April 2002 and October 2006. PARTICIPANTS: All 90 patients with CML in the chronic phase were selected from Union Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, and they were diagnosis based on the examinations of bone marrow morphologic, cytogenetics and/or molecular genetics. METHODS: All 90 patients with CML in the chronic phase were divided into two groups. 67 patients received oral STI571 (400 mg/day) in succession at the beginning time from April 2002 to June 2006, and the observation ended until October 2006, Blood routine will be done weekly, and bone marrow morphologic and cytogenetic examination would be done every three months. Other 23 patients selected from Union Hospital from March 1999 to April 2006 accepted allo-HSCT, with BuCy2 or modified BuCy2 as conditioning regimens. Cyclosporin A combining with short-term MTX were used in all patients for prophylaxis of graft-versus-host disease (GVHD). MAIN OUTCOME MEASURES: Hematology responses, eytogenetic response and two years survival in two groups were observed. RESULTS: Complete cytogenetic response was achieved in 60% and 100% of the patient treated with STI571 and transplantation respectively (P < 0.01). But two years survival of ST1571 and transplantation were 83.33% and 77.03% respectively, and no difference was found between the two groups (P > 0.05). No one died or discontinued therapy for adverse effects, and 4 out of 67 (5.97%) had grade 3 or 4 thrombocytopenia and/or leucopenia in the ST1571 group. Moreover, in transplantation group, 7 patients (30.4%) developed grade 2 to 4 acute GVHD, but 4 died of failed treatment. CONCLUTION: Compared with transplantation, patients treated with ST1571 achieved low complete cytogenetic responses and the treatment-related complications were mild and manageable or no need for treatment.