Background: Although busulfan-cyclophosphamide (BuCy) has been commonly used as a myeloablative conditioning (MC) regimen for allogeneic hematopoietic cell transplantation (HCT), a new MC regimen using busulfan-fludarabine (BuFlu) showed less regimen-related toxicities and lower non-relapse mortality (NRM) compared to BuCy in several non-randomized studies. Thus, we performed a prospective, multicenter, open-label, phase III trial to compare BuCy and BuFlu as a MC regimen for allogeneic HCT in leukemia and myelodysplastic syndrome. Methods: A total of 130 were enrolled between Nov 2005 and Sep 2009, but 4 patients were removed from the study and the remaining 126 patients were analyzed. Median age was 41 years (range, 17 to 59). Underlying disease was as followings: AML 70, ALL 47, CML 2, MDS 6, MDS/MPN 1. After random assignments, 64 patients received busulfan (3.2mg/kg/d x 4d) plus cyclophosphamide (60mg/kg/d x 2d) [BuCy arm] and 62 received busulfan plus fludarabine (30mg/m²/d x 5d) [BuFlu arm]. Results: Baseline patient and donor characteristics were well balanced between two arms. Five patients experienced engraftment failure (primary 1, secondary 4), which occurred only in BuFlu. Incidence and severity of acute GVHD, chronic GVHD, hepatic SOS, CMV disease, interstitial pneumonitis, and hemorrhagic cystitis were not significantly different between two arms. Adverse events (AE) within 100 days after HCT were graded using NCI CTCAE v3.0. Both upper and lower gastrointestinal (GI) AEs were more frequent in BuCy compared to BuFlu (P=0.018 for upper GI, P=0.050 for lower GI). NRM was similar between BuCy and BuFlu (13.4% vs. 22.3% at 1 year, P=0.291), whereas relapse-free survival in BuCy was higher than that in BuFlu (67.7% vs. 50.7% at 4 year, P=0.039). Thus, overall and event-free survivals in BuCy were significantly higher than those in BuFlu (overall, 51.1% vs. 36.1%, P=0.008; event-free, 46.2% vs. 33.3%, P=0.023). Conclusions: BuFlu caused less GI toxicities than BuCy, but NRM was similar. BuFlu showed lower survivals than BuCy mainly due to higher incidence of relapse. BuFlu cannot replace BuCy in patients who are eligible to myeloablative conditioning therapy before allogeneic HCT.