The objective of this study was to analyze the level of bcr-abl mRNA in peripheral blood (PB) after allogeneic stem cell transplantation (allo-SCT) in chronic myeloid leukemia patients, providing a experimental basis for diagnosing early relapse. bcr-abl mRNA levels in 78 PB and bone marrow (BM) samples from 15 CML patients after allo-SCT were detected by using real-time quantitative PCR. The results indicated that levels of bcr-abl mRNA before transplantation were high (median 29.303%) and decreased greatly (median 0) at the first month after allo-SCT. During the first year after allo-SCT, the patterns of serial bcr-abl transcripts varied in number, but the overall bcr-abl transcript levels significantly decreased at 6 months after allo-SCT. Majority of patients with undetectable or very low levels of bcr-abl mRNA were monitored after 1 year following transplantation. The hematological features of BM and PB in all detected patients remained normal. PB and BM bcr-abl values were not different significantly and had the similar trend of changes. It is concluded that the bcr-abl mRNA levels in CML patients change greatly early after allograft. Serial monitoring measurements for bcr-abl mRNA contribute to understanding the trend of change and effect of transplantation, also can be a guidance for starting therapy. But detectable levels of bcr-abl mRNA during the first 6 months do not indicate relapse. Measurements of bcr-abl mRNA of PB may be more suitable for routine monitoring long-term disease status in CML after allo-HSCT.