Myeloproliferative neoplasms (MPN) are clonal hematological malignancies that are frequently associated with an acquired somatic mutation in JAK2 (JAK2V617F). Patients with MPN are at a high risk of developing thrombotic events. Endothelial cell (EC) abnormalities are thought to contribute to this prothrombotic state. Budd–Chiari syndrome (BCS) and portal vein thromboses have been reported to be associated with JAK2V617F positive hematopoiesis. We explored whether JAK2V617F was present in ECs within the vessels of polycythemia vera (PV) patients with BCS using laser-capture microdissection followed by nested PCR or real-time RT-PCR. The presence of JAK2V617F in both ECs and hematopoietic cells belonging to BCS patients with PV indicates that ECs from these patients are involved by the malignant process and that in this subpopulation of patients the disease may originate from a cell common to hematopoietic and endothelial cells.