Myelodysplastic syndromes (MDS) are heterogeneous hematopoietic neoplasms characterized by ineffective hematopoiesis and a risk for progression to acute myeloid leukemia. A number of cytogenetic changes have been described that are characteristic to MDS and of clinical relevance; the specific gene targets of these alterations were largely unknown. On the other hand, over the past decade, technologies have been dramatically improved to enable high-throughput analysis of entire MDS genomes, leading to identification of frequent copy number neutral events and a number of novel gene targets implicated in the pathogenesis of MDS. In this review, we briefly overview the recent progress in the genetics of MDS, focusing on the newly identified gene targets in MDS.