Sixteen patients treated by allogeneic bone marrow transplantation (BMT) for chronic myelogenous leukemia (CML) were evaluated by the polymerase chain reaction (PCR) for bcr/abl-specific RNA transcripts at various time points after BMT. In reconstitution experiments, one CML cell per million normal mononuclear cells could be detected by direct agarose gel visualization of a bcr/abl-specific band following PCR. Bcr/abl message was found in ten out of 16 patients post-BMT. PCR-positive bcr/abl was present only transiently in three patients and correlated with relapse in three. One patient died in clinical remission, while two patients remain in remission despite persistence of bcr/abl-positive abl-positive cells at 180 days. Long-term follow-up of bcr/abl-positive patients in clinical remission may provide insight into the fate or residual Ph+ cells after BMT. This approach may aid in the identification of high-risk patients likely to relapse post-BMT.