Bone marrow BCR-ABL transcript levels were monitored serially by real-time quantitative PCR in 46 imatinib-treated chronic myeloid leukemia patients after achieving complete cytogenetic response (CCyR) for a median of 42 months (range: 9-53). Of 41 patients in continuous CCyR, 32 and nine could achieve a >/=3-log (MMoR group) or 2- to 3-log reduction (non-MMoR group), respectively. The MMoR group had a significantly lower recurrence rate of Ph+ metaphase than the non-MMoR group (6/32 vs. 7/9, P = 0.002), which was not significantly different between patients first achieving CCyR within or after 12 months of imatinib treatment (7/27 vs. 6/14, P = 0.086). Five patients suffered cytogenetic or hematological relapse. For all 46 patients, a >2-log reduction but not time when CCyR was first achieved was related to a lower relapse rate (1/42 vs. 4/4, P < 0.001). We concluded that the depth of BCR-ABL reduction after CCyR is more critical than when CCyR is first achieved. The kinetic pattern of BCR-ABL transcript is a good predictor of disease stability.