The kinetics of minimal residual disease (MRD) and chimerism were studied in 15 patients with chronic myeloid leukemia (CML) receiving nonmyeloablative stem cell transplantation (NST) and in 10 patients receiving conventional stem cell transplantation (CST). All NST patients showed T-cell mixed chimerism (MC) while granulocyte and B-cell MC occurred in 80% and 60% of the NST patients, respectively. In CST patients, T-cell MC was detected in 5 patients, of whom 3 were mixed only during the first month. MRD was detected in all NST patients. During the first 3 months the median BCR-ABL/ABL ratio was 0.2% in NST patients compared with 0.01% in CST patients (P < .01). However, 12 months after transplantation, the percentage of reverse transcriptase–polymerase chain reaction (RT-PCR)–positive patients was 20% in NST patients and 50% in CST patients. In conclusion, molecular remission can be induced in most patients after NST, albeit with different kinetics from CST.