The JAK2-V617F mutation is prevalent in almost all patients with polycythemia vera (PV) and about half of the cases of essential thrombocythaemia (ET) and primary myelofibrosis (PMF). A different allele burden in these entities has long been noticed, but little is known about its distribution among the neoplastic hematopoietic cell lineages within the bone marrow. We conducted a microdissection study of JAK2-V617F-mutated myeloproliferative neoplasms (MPN); 10 cases each of ET, PV, and PMF, with separate analysis of the JAK2 mutation status in three hematopoietic cell lines (i.e., megakaryo-, granulo-, and erythropoiesis). Different numbers of cell lineages harboring the JAK2-V617F mutation were found, being the lowest in ET (17/30), higher in PV (24/30) and in PMF (22/30). The megakaryopoiesis was the most commonly mutated cell lineage (24/30 cases). By analyzing microdissectates we were able to demonstrate a different allele burden of the JAK2-V617F mutation in the megakaryo-, erythro-, and granulopoiesis within the bone marrow of a given case of MPN. We demonstrated differences in the number of mutated cell lineages. The different mutation status may contribute to the different phenotypes of ET, PV, and PMF.