We here report the efficacy and toxicity of a conditioning regimen with fractionated 8-Gy TBI, fludarabine, and cyclophosphamide in allogeneic HSCT for pediatric hematological malignancies. Among 22 children who received related or unrelated HSCT, nine were transplanted with refractory disease and/or from HLA two or more loci-mismatched family donors. None of the patients developed graft failure. The Seattle grading system revealed that 18 patients had no RRT, and the remaining patients had grade I gastrointestinal toxicity alone. The estimated overall survival and leukemia-free survival at two yr were 57.1% and 48.0%, respectively, in 10 patients with acute lymphoblastic leukemia; 91.7% and 71.3%, respectively, in 12 patients with myeloid leukemia. The incidence of TRM was 4.8% at two yr. The rates of RRT above grade II and TRM in an 8-Gy TBI-containing regimen were significantly lower than the data of historical control patients who underwent 12-Gy TBI and cyclophosphamide with or without etoposide. The intermediate-dose TBI-based conditioning regimen may confer successful engraftment combined with minimized RRT, although its efficacy should be further evaluated.