The clonal blood disorders polycythemia vera, essential thrombocythemia and primary myelofibrosis belong to the BCR-ABL1-negative myeloproliferative neoplasms and are specified by increased production of terminally differentiated myeloid cells. Clonal evolution, disease initiation and progression are influenced by genetic alterations, often affecting cytokine signaling and gene expression. This review outlines somatic changes discovered in myeloproliferative neoplasms and how these genetic aberrations influence the pathogenesis of myeloproliferative neoplasms. Furthermore, genetic responses to drug treatments in myeloproliferative neoplasms are discussed.