Objective To investigate the significance of immunophenotype on the evaluation of myeloid dysplasia in patients with myelodysplastic syndromes (MDS). Methods Immunophenotype of myeloid cells in bone marrow of patients with cytopenia(s) and blast cells less than 5% were retrospectively analyzed by flow cytometry. Immunophenotype of patients with immune thromboytopenia were selected as the control. The abnormal myeloid immunophenptypes included abnormal sideward light scatter intensity, asynchronous antigen expression, cross-lineage antigen expression and abnormal pattern of the differentiation antigens. The results of immunophenotype were compared with morphology of myeloid cells. Results Among the total 255 cases, 127 patients were diagnosed as low-risk MDS, 95 patients were non-MDS, and 33 patients were idiopathic cytopenia of undetermined significance (ICUS). In MDS patients, the rate of abnormal immunophenotype (85.8%) was significantly higher than morphological dysplasia (57.5%) (P=0.000). In non-MDS patients, the rate of abnormal immunophenotype (1.1%) was significantly lower than morphological dysplasia (4.2%) (P=0.042). In ICUD patients without morphological dysplasia, abnormal immunophenotype could be detected in 48.5% patients. Conclusion Abnormal immunophenotype of myloid cells is helpful to early diagnosis and differential diagnosis of MDS.