This study was aimed to investigate the chimerism and fusion gene expression in patients with CML after allo-HSCT, to analyse engraftment and minimal residual disease by using STR-PCR combined with RT-PCR qualitative and quantitative assays, and to evaluate their clinical value for predicting disease relapse. 4 relapsed patients with CML after allo-HSCT were dynamically investigated. Qualitative analysis of donor chimerism was performed by multiplex PCR amplification of STR markers and capillary electrophoresis with fluorescence detection, qualitative detection of bcr/abl transcripts was performed by RT-PCR. The results showed that the 100% donor chimerism appeared in 4 patients on day 28 after transplantation and bcr/abl expression was negative, but the 4 patients were in status of unstable mixed chimerism (DC: 0% - 80.4%) at the different time points during the following up with bcr/abl gene positive. 2 patients of them were continuously mixed chimerism after relapse of CML, the other 2 changed from MC to CC by intervention of clinical treatment. Decreasing values of donor chimerism were detected prior to the occurrence of graft rejection and CML relapse, and bcr/abl gene expression was positive. It is concluded that the results of STR-PCR in the range of its sensitivity fully correspond with bcr/abl tests in patients. The combination of STR-PCR with RT-PCR will provide a highly sensitive and valuable tool for evaluating engraftment, graft rejection, and relapse and predicting GVHD. Furthermore, it can provide a basis for early intervention of clinical treatment, and can identify these high risk patients with molecular or cytogenetic relapse after allo-HSCT.