Objectives: Behçet’s disease (BD) is a chronic inflammatory disorder of still unknown etiology, characterized by endothelial cell injury/dysfunction and thrombosis and/or aneurysm of large blood vessels. Thrombophilia may play a role in the pathogenesis of thrombosis in BD. The common inherited gene defects, factor V (FV) 1691A (Leiden) and prothrombin (PT) 20210A, are known risk factors for thrombosis. The FV 4070G polymorphism was shown to influence circulating FV levels and to contribute to the activated protein C resistance phenotype. The aim of the study was to evaluate the role of FV 1691A, FV 4070G and PT 20210A gene mutations in Turkish BD patients with and without venous thrombosis. Methods: Seventy-one patients with BD (27 with venous thrombosis) and 91 healthy subjects were included in the study. FV 1691A, FV 4070G, and PT 20210A mutations were determined by a method based on PCR-RFLP. Results: The frequency of FV 1691A heterozygous mutation in BD patients with venous thrombosis (25.9%) was significantly higher than that in healthy subjects (8.8%; OR = 3.63; 95% CI 1.18–11.2). Although the frequency of this mutation in patients with venous thrombosis was higher than that in the patients without venous thrombosis (11.4%), the difference did not reach a statistically significant level (OR = 2.73; 95% CI 0.77–9.70). In BD patients with thrombosis, the frequencies of FV 4070G and PT 20210A were not significantly different compared to the BD patients without venous thrombosis and healthy subjects. Conclusions: Our results suggest that the FV 1691A, FV 4070G, and PT 20210A mutations are unlikely to play an important role in the pathogenesis of thrombosis in patients with BD.