This review focuses on the most recent literature concerning flow cytometry (FCM) application for diagnosis of myelodysplastic syndrome (MDS). Aberrant FCM results have been defined as abnormalities in at least three tested features comprising at least two bone marrow (BM) cell compartments. FCM results should be interpreted together with the BM smear cytology, the morphological assessment of BM biopsy, and cytogenetic results. Including FCM in the pre-treatment assessment may provide not only diagnostic but also prognostic information. Further studies are needed to evaluate the role of FCM in individual risk assessment for MDS patients and in therapy choice and/or follow-up.