The diagnosis of cytopenic patients suspected of myelodysplastic syndrome (MDS) can be challenging, particularly when initial laboratory assessments are indecisive. In normal haematopoiesis, the expression of differentiation antigens is tightly regulated. Changes in expression patterns may therefore indicate dysplasia, the hallmark of MDS. Multiparameter flow cytometry (MFC) can identify aberrancies in differentiation antigen expression and maturation patterns not recognized by cytology. MFC performed according to recommendations defined by the International and European LeukemiaNet-associated Working Group focusing on standardisation of MFC in MDS (iMDSFlow) may reveal aberrancies in the myeloid progenitor cells, B-cell progenitors, maturing myelomonocytic cells and erythroid cells. Defined abnormalities can be counted in MFC scoring systems to provide a means to determine the extent of dysregulation of the maturation patterns, i.e. dysplasia according to MFC. Ideally, scores should enable a categorization of MFC results from bone marrow assessments in cytopenic patients as ’normal’, ’low probability of’ or ’high probability of’ MDS. Notably, MFC as a single technique is not sufficient for the diagnosis of MDS, and results should always be evaluated as part of an integrated diagnostic workup.