Twelve children with high-risk acute lymphoblastic leukemia underwent stem cell transplantation (SCT) with a conditioning regimen consisting of busulfan, cyclophosphamide and thiotepa. Eight of them underwent SCT while in complete remission (CR) and the other 4 while not in CR. Three children underwent HLA-matched related bone marrow transplantation (BMT), 7 HLA-matched unrelated BMT, 1 HLA one-locus-mismatched unrelated cord blood cell transplantation, and 1 autologous peripheral blood stem cell transplantation. Grade II-IV acute GVHD was observed in 3 of the 11 allo-SCT cases, while chronic GVHD was seen in 3 of 9 evaluable cases. None of the 12 cases showed thrombotic microangiopathy, and veno-occlusive disease (VOD) was observed in 3. Nine of the patients are alive and disease-free 6-45 months after diagnosis. The event-free survival rate at 3 years was 72.2% for the 12 patients, including 8 of the 9 who received SCT during CR, and 2 of the 4 who did so while not in CR. The other 3 patients died: 2 of disease progression and 1 of VOD with pneumonia. All of those who died had undergone unrelated BMT.