The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal myeloid haemopathies characterized by defective differentiation of hematopoietic cells and expansion of the abnormal clone. This leads to the bone marrow failure with resulting peripheral blood cytopenias and evolution to or toward acute myeloid leukaemia that characterise MDS clinically. The clinical heterogeneity of MDS has led several groups to analyse patient and clinical characteristics to develop prognostic scoring systems yielding estimates of overall and leukaemia-free survival to guide clinical decision-making. These models have evolved over time as our understanding of the pathogenesis, natural history, and treatment of MDS has improved. Rapid advances in flow cytometric analysis, adjuncts to standard metaphase cytogenetics, and gene mutation analysis are revolutionizing our understanding of MDS pathogenesis and prognosis. Despite the existence of multiple well-validated prognostic scoring systems, further needed refinements of current models with these new sources of prognostic data are described.