A retrospective investigation of the JAK2 V617F mutation was carried out in DNA samples from 131 bone marrow (BM) core biopsy specimens corresponding to patients with polycythemia vera (PV) (n = 31), essential thrombocythemia (ET) (n = 31), chronic idiopathic myelofibrosis (CIM) (n = 18), as well as patients with normal BM and secondary reactive hyperplasia. We used the TaqMan polymerase chain reaction single nucleotide polymorphism genotyping assay to detect the specific JAK2 mutation. This technique allowed us to detect the JAK2 V617F mutation in a population containing at least 5% of homozygous mutants. Overall, the incidence of the JAK2 V617F mutation was 87% in PV, 67% in ET, and 66% in CIM. This approach proved to be reliable and more sensitive in detecting the mutation compared with that of initial studies on different materials but similar to that of recent work with various polymerase chain reaction-based techniques. Two essential findings arose from our study. First, this technique could be carried out with DNA samples, even partially degraded, from routinely processed BM core biopsy specimens. Second, after correlation with morphological features, it turned out that the characteristics of the megakaryocytes were more specific than the mutational status of JAK2 in characterizing ET and CIM. Concerning PV, as expected, the incidence of the JAK2 mutation was higher, but the morphological criteria were misleading in some cases, strongly suggesting that the combination of both histologic and molecular data would enable the characterization of virtually all cases.