Myelodysplastic syndromes (MDS) are malignant disorders of hematopoietic cells. For many neoplasms, immunophenotype data of the neoplastic cells provide valuable information in clinical practice. However, the clinical values of immunophenotype data have not yet been firmly established for MDS. Since MDS blasts are not predominant in the bone marrow and peripheral blood, which makes reliable immunophenotyping of blasts difficult, we used a newly developed density-centrifugation reagent to generate blast-enriched MDS samples for phenotyping. The key findings of our study, which phenotyped blasts from 116 patients with MDS or acute leukemia transformed from MDS, were the following. (1) MDS blasts were usually CD34( + )CD38( + )HLA-DR( + )CD13( + )CD33( + )CD2(-)CD3(-)CD5(-)CD8(-)CD19(-)CD20(-) in flow cytometric analysis and often lacked myeloperoxidase in cytochemistry, regardless of the MDS subtype. (2) MDS blasts showed asynchronous expression of antigens (expression of both stem cell antigens and antigens of mature myeloid cells). (3) During disease progression of MDS, phenotypic clonal evolution (transition from blasts with a relatively mature phenotype to blasts with a more immature phenotype) occurred in at least some cases. (4) CD7-positivity was an independent variable associated with a short survival in MDS. Further studies of blast immunophenotypes will deepen our understanding of MDS and hopefully improve the clinical approach to these intractable disorders.