Myelodysplastic syndrome (MDS) is a heterogeneous disease characterized by dysplasia and ineffective hematopoiesis. The dysplasia is crucial in the diagnosis of MDS, but the morphologic abnormalities of bone marrow cells are not specific for MDS. When the morphological evaluation of marrow dysplasia and cytogenetics can not give enough informations, for diagnosis of MDS, the application of flow cytometry (FCM) for immunophenotyping in MDS will become particularly important. Multiparametric evaluation of myeloid, monocytic maturation and antigen expression pattern contribute to the identification of two or more aberrancies in MDS cases. FCM evaluation of erythroid dysplasia is particularly difficult, because of the limited availability of specific markers. By analyzing the proteins involved in cellular iron metabolism, MDS erythroid cells present an "iron-loaded" phenotype characterized by increased ferritin contents and reduced transferrin receptor, which reflects the degree of dysplasia assessed by morphology. The proportion of CD34(+) cells increased, abnormal expression of surface antigen is also important. The application of flow cytometry in detecting dysplasia of myelodysplastic syndrome is discussed in this article.