Patients suffering from Philadelphia chromosome-negative chronic myeloproliferative disease (Ph(-) CMPD), such as polycythaemia vera (PV), are frequently JAK2(V617F)-mutated and have an elevated risk for thromboembolic complications. Recent data indicated that the molecular basis of JAK2(V617F) and thrombosis might be related to increased expression of CD239, the Lutheran blood group/basal cell adhesion molecule, in PV-derived red blood cells. The aim of this study was to clarify whether JAK2(V617F) PV with thromboembolism is characterised by CD239 overexpression. Leukocyte-derived JAK2(V617F) was detectable in bone marrow cells but also in liver and spleen explants and transplants after thrombosis (95% JAK2(V617F)-positive Ph(-) CMPD, n = 66). CD239 was expressed in a constitutive fashion in PV-derived bone marrow cells and thus a pro-thrombotic function does not seem to be mediated by increased CD239 expression alone.