In the myelodysplastic syndromes (MDS), the haematopoietic cells show various levels of abnormal maturation and differentiation, which can be detected by flow cytometry. Testing the anomalies of stage- or lineage-specific surface antigens in CD34+ blasts can distinguish MDS from non-clonal cytopenic diseases, and also reflect the pathological characteristics of MDS as a class of clonal diseases for providing new clues to basic research. The present study established a flow cytometric scoring system (FCMSS) based on theproportion and antigenic co-expression of CD34+ blasts. This FCMSS showed good sensitivity and specificity (77.8% and 100%) in the assisted diagnosis of low-risk MDS without chromosome anomalies, ringed sideroblasts and excess marrow blasts. Moreover, we explored and reported different modes of abnormal expression of CD34+ blasts antigens in different disease stages and analyzed the biological significance of the immunotypes for the first time. We found expression of mature myeloid antigens and lymphoid antigens gradually decreased, and early functional antigens gradually increased from low-risk MDS with normal karytype to low-risk MDS with abnormal karyotype then to high-risk MDS. The patients with higher FCM scores were generally accompanied with HLA-DR15 allele or hypocellular marrow. Evolution of clones and immunological factors might have influence on expression of antigens in CD34+ blasts.