Myelodysplastic syndrome (MDS) is a kind of clonal stem-cell disorder in which aberration within a hematopoietic stem cell (HSC) gives rise to the entire disease as in acute myeloid leukemia (AML). Studies have showed that contrasting normal stem cells, AML stem cells express CD96 and CD123, but lack of CD90, although both of them reside within the CD34(+)CD38(-) population. So far, little is known about expression of the markers on MDS HSC. In this study, we analyzed the immunophenotypic characteristics of CD34(+)CD38(-) bone marrow (BM) cells by multicolor flow cytometry in 38 patients with MDS and 10 control patients. We found that CD34(+)CD38(-) BM cells coexpressed CD13, CD33, CD117, CD133, and HLA-DR almost in all patients, but in MDS they expressed higher amounts of CD13 (79% +/- 16% vs. 36% +/- 13%, P < 0.05) and CD133 (66% +/- 20% vs. 25% +/- 13%, P < 0.05). CD90 was expressed in all control patients but just in 63% of patients with MDS. No control patients had an expression of CD2, CD5, CD7, CD44, CD96, and CD123, which expressed variable amounts in 17-53% of patients with MDS. The level of CD13 in RCMD (89% +/- 7%), RAEB-1 (88% +/- 11%), and RAEB-2 (81% +/- 13%) were obviously higher than that of RA (63% +/- 16%, P < 0.05). CD2, CD5, and CD7 were more frequently observed in RAEB or INT and HIGH-R cases. Taken together, we demonstrate MDS stem cells display deranged phenotypic abnormalities that may make them particularly difficult to eradicate using therapies targeted against surface antigens, and the percentage of cells expressing CD13 is notably higher in patients with high-grade MDS that may be a potential prognostic indicator of MDS in the future.