Bone marrow samples of 70 transplant recipients with CML were studied by Southern blot analysis and RT-PCR using a two-step procedure with nested primers. Twenty-two patients were studied once and 48 were assessed on multiple occasions. All patients remained in a hematological remission during the study. The time of follow-up after the transplant ranged from 2 to 144 months with a median of 42 months. Thirty-nine patients (56%) were negative by RT-PCR and Southern blot studies at the time of their last evaluation. The proportion of RT-PCR negative patients increased with the duration of follow-up after the transplant; 36% of patients were RT-PCR negative after 1 year compared with 60% after 2 years and 78% after > or = 5 years. Patients maintained on immunosuppression had a higher probability of remaining RT-PCR positive. Age, sex, time from diagnosis to BMT, as well as acute and chronic GVHD did not influence the RT-PCR status. The majority of patients studied on multiple occasions demonstrated a stable RT-PCR and Southern blot pattern. Some showed uni- or multi-directional transitions. However, none of the patients studied progressed to a hematological relapse. RT-PCR studies on colonies grown from RT-PCR positive. Southern blot negative patients confirmed that some of the clonogenic progenitors are able to produce BCR/ABL transcripts.