In order to evaluate relapse predication ability of STR-PCR combining with qualitative RT-PCR for the bar/abl transcripts to the patient with chronic myeloid leukemia (CML) fulfilled allogeneic stem cell transplantation (allo-HSCT), 24 patients with CML after allo-HSCT were dynamically investigated for MRD, quantitative 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 detected by nested RT-PCR. The results showed that persistent full donor chimerism (DC >/= 95%) was associated with an absence of MRD. All patients with stable MC (90% </= DC < 95%) and bcr/abl negative had a probability of long-term survival with molecular remission, however the result of bcr/abl positivity was not always associated with leukemia relapse, only the patient with decreasing values of donor chimerism as well as bcr/abl positive proved to be in a higher risk of relapse or graft failure. Decrease of donor chimerism in correlation with MRD positive was detected in 5 patients. Three out of five patients had been proved to have a molecular relapse, one out of five patients had developed to cytogenetic relapse and another patient experienced graft failure. 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 MRD detection in CML and can identify these high risk patients with molecular or cytogenetic relapse after allo-HSCT.