Myelodysplastic syndromes are a heterogeneous group of clonal bone marrow disorders characterized by dysplasia, progressive bone marrow failure, and increased risk of transformation to acute myeloid leukemia. Although diagnostic criteria are well established, a diagnosis based on morphologic and cytogenetic findings is often difficult in a significant number of patients. Multiparametric flow cytometric immunophenotyping is a highly sensitive and specific method for quantitative and qualitative evaluation of hematopoietic cells. Flow cytometry is used to identify dysregulated antigen expression of myeloid cells, estimate the proportion of bone marrow blasts cells, and reveal their abnormal immunophenotype. Recent data suggest that flow cytometry adds important prognostic information to the widely accepted International Prognostic Scoring System.