Detection and monitoring of minimal residual disease has become one of the most prevalent topics in chronic myeloid leukemia(CML) therapy. The goal of early detection of residual disease is to allow timely therapeutic intervention before overt relapse of therapy resistant disease occurs. The most powerful tool to serve this purpose is polymerase chain reaction (PCR). Major improvements in assay techniques have advanced PCR from a purely qualitative test with considerable variability of test results to a real-time quantitative assay with far more reproducible results than were possible before. At the same time, treatment of CML has changed dramatically since the introduction of imatinib. Integration of therapy and molecular assays such as PCR, in addition to a profound understanding of the pathophysiology of CML, has assumed even more importance. Quantitative PCR testing has become the standard monitoring strategy for patients undergoing stem cell transplantation. Although correlations have been established between positive test results and probability of relapse, no absolute guidelines for monitoring exist, especially for patients treated with imatinib.