Acute myeloid leukemia (AML) patients with chromosome 11q23 abnormalities or MLL rearrangements have a poor prognosis when treated with conventional chemotherapy. However, the efficacy of allogeneic bone marrow transplantation (BMT) for this type of leukemia is not yet clear. We describe 2 MLL-AF6 fusion transcript-positive AML patients treated with allogeneic BMT who were monitored for minimal residual disease (MRD) by reverse transcriptase polymerase chain reaction. Although long survival or cure of this type of AML is rarely reported, 1 patient had durable remissions. Fusion transcripts disappeared in 1 patient but not in the other, even after the graft-versus-host disease effect was increased by the discontinuation of immmunosuppressive therapy. This is the first report of MRD and the probability of graft-versus-leukemia effects following BMT in AML patients who are MLL-AF6 fusion transcript positive.