Myelodysplastic syndromes (MDS) are diagnosed by a combination of cytomorphology and cytogenetics. Fluorescence in situ hybridisation (FISH) can accompany cytogenetic results or can in some cases also be performed instead of chromosome banding analysis. In recent years also immunophenotyping added important information for the diagnosis of MDS. So far, diagnosis however still depends on cytomorphology of peripheral blood and bone marrow smears. The prognostication is done according to the IPSS or very recently to the revised IPSS by a combination of cytopenia, morphologic features according to the WHO classification (2008) and cytogenetic results. In addition, also molecular markers have been shown to contribute important information for diagnosis and also for prognosis in patients with MDS. These markers are in some cases found by next generation sequencing including whole exome sequencing of patients with MDS. Prospective analysis will show the best combination of methods to diagnose patients with MDS or to define their respective prognosis. Without doubt, mutations in newly depicted genes, including genes involved in the spliceosome, will be included in the management of MDS patients.