In the present study, we compared the incidence and severity of oral mucositis among patients undergoing allogeneic hematopoietic stem cell transplantation after fludarabine-based regimens with busulfan 12.8 mg/kg (FB12.8), with busulfan less than or equal to 9.6 mg/kg (FB9.6), and with melphalan 140 mg/m2 (FM). The incidence of oral mucositis after FB12.8 was the highest among these 3 groups. After FM, all of the patients had developed oral mucositis by day 7. The mean disease duration of oral mucositis after FB12.8 was 13.5 days, whereas the mean disease duration after FM was 24.9 days, and was significantly prolonged as compared to that after FB12.8 (p=0.0009). The incidence of severe oral mucositis (grade 3) after FM was significantly higher than that after FB12.8 (p=0.03). As stated above, although the incidence of oral mucositis after FB12.8 was higher than that after FM, oral mucositis after FB12.8 showed improvement relatively quickly without deterioration. In contrast, the higher incidence of severe oral mucositis and the delay in resolution of mucositis after FM were remarkable.