Objective To evaluate the fludarabine instead of cyclophosphamide in modified busulfancyclophosphamide (mBuCy) regimen as a new myeloablative conditioning regimen for the treatment of acute leukemia patients receiving allogeneic hematopoietic stem cell transplantation (HSCT).Methods The clinic data of 45 acute leukemia patients undergoing allogeneic HSCT were analyzed.Among them,23 patients received mBuCy as conditioning regimen and 22 patients received BuFlu regimen (fludarabine 40 mg·m-2·d-1 for 5 days,instead of cyclophosphamide in mBuCy).Hematopietic engraftment,regimen-related toxicity (RRT),graft-versus-host disease (GVHD),infection condition,non relapse mortality,and overall survival were compared between the two groups.Results All patients achieved hematopoietic reconstitution and complete donor chimerism except for one patient of mBuCy group died of cerebral hemorrhage during conditioning.The incidence of RRT was no significant differences (P ＞ 0.05).In BuFlu group,the incidence of virus infection was higher (P =0.009),and the incidence of Ⅲll-Ⅳ aGVHD were 26.l ％ (6/23) and 4.5 ％ (1/22) (P =0.046) in mBuCy and in BuFlu group respectively.With a median follow up of 41 months,the incidence of non relapse mortality in mBuCy group was 17.4 ％ (4/23) and in BuFlu group was 9.1％ (2/22) (P =0.665).In mBuCy group and in BuFlu group,the relapse rates were 30.3 ％ (7/23) and 40.9 ％ (9/22) (P =0.474),the 5-year overall survival rates were (55.1±11.9) ％ and (61.4±10.8) ％ (P =0.659),and disease-free survival rates were (44.5±12.1) ％ and (22.1±12.3) ％ (P =0.747),respectively.Conclusions Fludarabine instead of cyclophosphamide in mBuCy regimen as a new myeloablative conditioning regimen has well tolerance,lower incidence of sever GVHD,satisfied overall survival,but the risk of infection and replase should be considered.