In order to investigate the features of M-bcr/abl and m-bcr/abl fusion transcripts in patients with chronic myeloid leukemia (CML) after allogeneic stem cell transplantation (SCT), M-bcr/abl and m-bcr/abl fusion transcripts were sequentially detected by RT-PCR technique in 72 CML patients after SCT. The results showed that M-bcr/abl positive rate (79.2%, 42/53) within 6 months after SCT was remarkably higher than that in 6-12 months group (34.3%, 11/32) and >or= 12 months group (35.1%, 13/37) (P < 0.001), and the clinical relapse rates in corresponding periods were 1.9% (1/53), 0% (0/32) and 16.2% (6/37) respectively. M-bcr/abl and m-bcr/abl fusion transcripts occurred in 5 of 6 clinically relapsed patients. In period of more than 6 months after transplantation, none of 17 M-bcr/abl(+) samples from 14 patients in cytogenetic remission appeared positive reaction of m-bcr/abl. It is concluded that M-bcr/abl(+) fusion transcript still existed in most patients after SCT, and usually disappeared within 6 months. Existence of M-bcr/abl is not a clinical relapse marker in CML patients. Simultaneous detection of M-bcr/abl and m-bcr/abl fusion transcripts can be helpful for monitoring residual disease.