Myelodysplastic syndromes (MDS) are clonal hematologic neoplasms that can result in cytopenias and increase the risk of leukemic transformation. The disease is characterized by several recurrent cytogenetic defects, which can affect diagnosis, prognosis, and treatment. Metaphase cytogenetics (MC) is the gold standard in karyotypic analysis in hematology. Progress in molecular analysis, including additional karyotypic tools exemplified by fluorescence in situ hybridization, comparative genomic hybridization, and more importantly, single nucleotide polymorphism array (SNP-A) analysis, has led to increased detection of chromosomal abnormalities in myeloid malignancies and improved prognostic risk stratification. SNP-A, together with MC, has also been instrumental in the discovery of genes that have improved our understanding of the biology of MDS. Newly elucidated molecular abnormalities in MDS include mutations in CBL, TET2, ASXL1, IDH1/IDH2, EZH2, DNMT3A, and UTX. This review provides an update on the changing landscape of molecular and cytogenetic characterization in MDS and its significance in disease biology and clinical practice.