Chronic myeloid leukemia (CML) is characterized by BCR-ABL translocation and an increased number and migration of immature myeloid cells into the peripheral blood. The detection limit of the BCR-ABL transcript, particularly after treatment, is controversial. In the present study, we used quantitative real-time reverse transcription-polymerase chain reaction (RT-qPCR) to monitor BCR-ABL expression in Moroccan CML patients undergoing imatinib treatment, and compared the results with those of conventional PCR and fluorescence in situ hybridization (FISH). The aim of this study was to establish a new molecular tool for in vitro diagnosis of CML. In a retrospective comparative analysis, 20 CML Moroccan patients who had received imatinib treatment (N = 20) were analyzed by real-time PCR, conventional RT-PCR, and FISH. Half of the samples analyzed (N = 10) were positive for BCR-ABL gene expression, while the other half (N = 10) were negative according to conventional PCR. Interestingly, 5 of the 10 samples shown to be negative by conventional PCR showed positive expression of the BCR-ABL gene according to RT-qPCR. The RT-qPCR results were confirmed by FISH, which revealed a high concordance (100%) rate. We found that real-time RT-qPCR is more reliable and should be used in Moroccan biomedical analysis laboratories to monitor CML progression, particularly for minimal residual disease, following imatinib treatment.