OBJECTIVE To evaluate the values of immunophenotyping in the diagnosis and prognosis of myelodysplastic syndromes (MDS). METHODS Surface markers of mononuclear marrow cells were analyzed by indirect immunofluorescence for a panel of monoclonal antibodies in 32 patients with MDS. RESULTS Expression of myeloid antigen increased significantly while lymphoid antigen decreased. The antigen expression was correlated with the FAB subtype of MDS, Immature myeloid cells (CD13+, CD33+) was being increased and the lymphoid antigen expression decreased with the RA/RAS evolving to RAEB and RAEB-t. Compared with normal marrow, the number of CD34+ cells was not significantly different in RA/RAS subtypes but significantly higher in RAEB/RAEB-t subtypes. The expression of early marrow cell antigens (CD38, HLA-DR, CD99R and CD9) was significantly increased. The expression of CD34 and other early antigen was predictive for transformation and poor survival. CONCLUSION Surface marker analysis of mononuclear marrow cells may be a useful tool for the diagnosis and prognosis of MDS.