The Janus kinase 2(V617F) (JAK2(V617F)) mutation is an acquired genetic defect that is considered to enhance thrombosis in Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs). Thrombosis is also a well-defined component of Behcet syndrome (BS). The aim of this study was to determine the frequency of JAK2(V617F) mutation in BS-associated thrombosis. A total of 152 patients with BS (62 with thrombosis and 90 without thrombosis) were enrolled. An additional 186 patients with MPNs and 107 healthy blood donors were included to serve as diseased and healthy controls, respectively. None of the patients with BS and healthy controls carried the JAK2(V617F) mutation, whereas 67% of patients with MPNs were positive for JAK2(V617F). The frequency of thrombosis in patients with MPNs was not statistically different between carriers and non-carriers of JAK2(V617F) mutation. Our data suggest that JAK2(V617F) is not directly related to thrombosis in MPNs and in other thrombotic entities, such as BS.