Evaluation of minimal residual disease (MRD) provides prognostic information on various hematological malignancies. We describe here the prognostic efficacy of real-time quantitative polymerase chain reaction (RQ-PCR)-based analysis of major bcr/abl mRNA in cases of Philadelphia chromosome-positive leukemia (Ph-leukemia). Twenty-one patients with Ph-leukemia were enrolled as subjects to determine the usefulness of RQ-PCR-based measurement of bcr-abl/abl ratios. Imatinib mesylate (imatinib) was administered to seven of the 21 patients before allogeneic stem cell transplantation (SCT). Hematological relapse or failure of treatment with SCT was observed in 2 of those patients who showed bcr-abl/abl ratios of more than 0.002%, and 5 of the 7 patients showed both RQ-PCR and RT-PCR negativity immediately after SCT. All of the 5 patients who did not receive imatinib before allogeneic SCT showed RQ-PCR negativity immediately after SCT, but the results of RT-PCR were positive in 3 patients at the same time points, and those became negative after donor lymphocyte infusion or the appearance of graft-versus-host disease. Administration of imatinib before SCT was thought to induce an early remission. On the other hand, 8 patients who received imatinib without SCT showed a remarkable decrease in bcr-abl/abl ratios. The ratio gradually rose in one patient with Ph+ALL, enabling prediction of the hematological relapse preceding detection by fluorescence in situ hybridization (FISH) analysis. Standardization of RQ-PCR analysis of bcr-abl mRNA will help to predict early hematological relapse in patients with MRD. In conclusion, it is thought that measurement of RQ-PCR-based major bcr/abl mRNA in patients who were given imatinib and were treated with SCT is useful for the evaluation of MRD and in deciding additional treatment.