Activation of the JAK-STAT pathway by driver mutations of JAK2, CALR or MPL is the pathogenesis of myeloproliferative neoplasms (MPN). Mutations in epigenetic regulators that often coexist with driver mutations reinforce the function of MPN initiating cells and support MPN onset and maintenance. In myelofibrosis patients, JAK2 inhibitors exerted an innovative therapeutic effect on splenomegaly and constitutional symptoms, but had minimal effects on the JAK2V617F allele burden. Epigenetic abnormalities may be a good target for novel therapeutic strategies aiming to induce molecular remission in myelofibrosis patients. New information obtained by next-generation sequencing technologies would greatly contribute to elucidation of the mechanisms underlying MPN onset, progression and leukemic transformation.