Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms. With the emergence of therapeutic options, attempts to standardize diagnostic, prognostic and response criteria to guide treatment decisions are increasingly important. This has been achieved in part by the revised 2008 World Health Organization classification and consensus guidelines outlining refined definitions and standards. Conventional criteria have limitations in terms of sensitivity and specificity. Multiparameter flow cytometry (FC) can be used real-time, and is a highly reproducible and objective way of assessing the pattern of expression of multiple antigens on a single hematopoietic cell and defined subpopulations. By comparing antigen expression within maturing myelomonocytic populations with that identified on the equivalent normal cells, abnormalities identified may provide a diagnostic indication of stem cell dysmaturation. There are now increasingly robust data demonstrating the capacity of FC to discriminate MDS from non-clonal cytopenias and dysplasia, as well as further refine disease classification and prognostication, which will be reviewed here.