Essential thrombocythemia is a clonal stem cell disorder whose clinical course is dominated by a high incidence of thrombotic and, to a lesser extent, hemorrhagic complications. Although a proportion of patients remain asymptomatic and suffer no vascular events, there is also a long-term risk of transformation to acute leukemia or myelofibrosis. Recent major advances in this field include the discovery of the V617F JAK2 mutation in many patients and MPL515L or K mutations in a smaller minority. The results of the Medical Research Council Primary Thrombocythemia 1 trial published in 2005 have also informed clinical management. This review focuses on the impact of these findings upon current thinking in terms of pathogenesis and classification of the myeloproliferative disorders and highlights controversies in these areas as well as in diagnostic criteria and disease management.