Allo-SCT is the only potentially curative regimen for myelodysplastic syndromes (MDSs), but it is associated with a high relapse risk. The role of chimerism analysis for prediction of relapse is yet to be determined. To assess the clinical usefulness of mixed chimerism (MC) for predicting hematological relapse, 75 consecutively transplanted patients with MDS were analyzed with regard to lineage-specific chimerism, encompassing CD33(+) cells in peripheral blood (PB, n=49) and CD34(+) cells in BM (n= 35). A cutoff of 5% recipient cells was used to discriminate complete donor chimerism from MC. A total of 19 patients (25%) experienced hematological relapse after a median of 5 (1-31) months. Sensitivity for detection of relapse was 59% for CD33(+) PB cells and 92% for CD34(+) BM cells with corresponding specificities of 91% and 65%. CD34(+) BM cells were analyzed before relapse in seven patients, five of whom showed MC at a median of 2.5 (0.5-7) months before relapse. In contrast, 8 of 18 patients showed MC involving CD33 PB with a median of one month (0.5-2) before relapse. Here, we provide a model for early detection of relapse after SCT in MDS, in which serial characterization of both CD33(+) PB cells and CD34(+) BM cells gives an opportunity for early treatment before overt relapse.