A 4-year-old boy with Down syndrome (DS) was diagnosed as having acute monoblastic leukemia (AML-M5a). Leukemic cells were CD33+, CD56+ and CD4+, with t(9;11) on cytogenetic analysis and MLL gene rearrangement. After 2 courses of induction therapy using an AML 99-Down protocol failed to obtain complete remission, the patient received cord blood transplantation from an HLA-matched donor (CBT) following a conditioning regimen comprising total body irradiation and cyclophosphamide. Only cyclosporin A was used for graft-versus-host disease prophylaxis. Stem cell transplantation may not be indicated for AML patient with DS in first remission, who display a high rate of life-threatening and fatal toxicity on therapy. This patient remained well controlled in complete remission for 4 years, representing a rare case of DS with chemotherapy-resistant AML successfully treated with a CBT.