Molecular monitoring of BCR-ABL transcript levels by real-time quantitative PCR is increasingly used to assess treatment response in patients with chronic myeloid leukaemia (CML). This has become particularly relevant in the era of imatinib therapy when residual levels of leukaemia usually fall below the level of detection by bone marrow cytogenetic analysis. Studies of imatinib-treated patients have determined that BCR-ABL levels measured early in therapy can predict subsequent response and the probability of acquired resistance. The defining of a molecular level of response that indicates a high probability of progression-free survival highlights the relevance of molecular analysis for clinical management. Small increases in the BCR-ABL level can identify patients with kinase domain mutations that lead to imatinib resistance. Therefore, these assays can be used as a screening strategy for mutation analysis. As second generation kinase inhibitors commence clinical trials, the molecular response will be a primary end-point that determines efficacy.