Abstract: Objective To compare BFA (busulfan, fludarabine plus cytarabine) with BuCyA (busulfan, cyclophoshpamide plus cytarabine) as the conditioning regimens in allogeneic stem cell transplantation for acute leukemias. Methods 83 patients with acute leukemia were allocated to BFA group 〔busulfan 3.2 mg/(kg·d), -9 d-6 d; fludarabine 30 mg/(m 2 ·d),-5 d--1 d; cytarabine, 1 g/(m 2 ·d), -5 d--1 d〕 or BuCyA group 〔busulfan, 3.2 mg/(kg·d), -8 d--5 d; cyclophoshpamide 60 mg/(kg·d),-2 d--1 d; cytarabine, 3 g/(m 2 ·d),-4 d--3 d〕. Their three-year disease-free survival (DFS) rate, complete remission (CR) rate and incidences of acute graft versus host disease (aGVHD) and hemorrhagic cystitis were monitored. Results BuCyA group had lower DFS (40.0% vs 61.9%, P=0.039 9) and lower CR (44.0% vs 71.6%, P=0.031 0) than BFA group. About 20% of patients treated with BuCyA were not in remission, compared with 51.6% of those treated with BFA. aGVHD occurred in 46.7% patients in the BuCyA group and 50.9% patients in the BFA group, which were 23.3% and 9.4%, respectively, for those graded Ⅲ -Ⅳ. Severe infection occurred in 23.3% patients in the BuCyA group and 22.9% patients in the BFA group. Severe bleeding occurred in 26.7% patients in the BuCyA group and 11.4% patients in the BFA group. The incidence of hemorrhagic cystitis in the BuCyA group and BFA group was 16.7% and 5.7%, respectively. Conclusion BFA is a safer and more effective conditioning regimen compared with BuCyA.