Abstract: The reverse transcriptase‐polymerase chain reaction (RT‐PCR) was compared with fluorescence in situ hybridization (FISH) and real‐time quantitative RT‐PCR (RQ‐PCR) for minimal residual disease (MRD) monitoring in 266 post‐transplant bone marrow samples from 78 patients with chronic myelogenous leukemia (CML). The sensitivities of FISH to BCR‐ABL positive samples determined by first‐round (1st) RT‐PCR, second‐round (2nd) RT‐PCR, and RQ‐PCR were 64.2%, 25.8%, and 20.7%, respectively. The BCR‐ABL/ABL ratio by RQ‐PCR had a mean of 0.000 13 in the 1st RT‐PCR‐negative samples and 1.42 in the 1st RT‐PCR‐positive samples (P<0.001), and means of 0.000 39 and 0.51 in the 2nd RT‐PCR‐negative and ‐positive samples (P< 0.001). The mean ratios of BCR‐ABL/ABL by RQ‐PCR were significantly different in N/N (1st/2nd RT‐PCR) or N/P and P/P (P<0.001), but not in N/N and N/P, which showed that the discriminative power of RQ‐PCR is confined to the 1st RT‐PCR level. In this respect, monitoring of the 1st RT‐PCR might be useful for estimating normalized BCR‐ABL levels after transplantation. Nested RT‐PCR was of limited use, as RQ‐PCR quantified the BCR‐ABL transcripts in 60 (91%) of 66 samples determined to be negative by 2nd RT‐PCR. FISH was significantly correlated with RQ‐PCR in FISH‐positive samples (n=24, r=0.79, P=0.001). An increase of FISH preceded that of RQ‐PCR in a few cases with molecular relapse. By analyzing a large number of samples post‐transplant, we found that RQ‐PCR might be the most useful assay for MRD monitoring; however, FISH and RT‐PCR were found to be useful complementary tools.