The World Health Organization introduced flow cytometry as an additional criterion for diagnosis of myelodysplastic syndromes (MDS). Aberrant antigen expression on bone marrow (BM) blasts may identify "low-grade MDS." This study aimed to examine differences in antigen expression on CD34+ BM cells between patients with MDS and those with secondary cytopenia. BM aspirates of 175 patients with cytopenia were classified as MDS or secondary cytopenia. Expression of stem cell antigens (CD34, CD133), myeloid antigens (CD13, CD33), B-cell antigens (CD19, CD10), growth factor receptors (CD117, CD123), and chemokine receptor (CD184) was examined. Thirty-two normal adults and 49 patients with CD34+ acute myeloid leukemia (AML) were also examined. High percentage of CD34+ cells, CD117 and CD123 overexpression, and abnormal CD45 expression on these cells are the best markers for MDS. These phenotypic aberrancies correlate with number of blasts and degree of dysplasia, and were similar to those in CD34+ AML, thus reflecting the relationship between these disorders.