To determine the relation between factor V Leiden and Behçet's disease (BD), which is described as chronic relapsing vasculitis with pathogenetic mechanisms that seem to be related to anticoagulant pathways. Using polymerase chain reaction, the factor V Leiden mutation was investigated in 44 patients with BD, of which 5 had thrombotic histories. Ten patients were found to have the factor V Leiden mutation. This frequency (22.7%) was higher than that of our general population (7.1 %) (p < 0.05). Of the 5 patients with BD with thrombotic histories, 3 (60%) had factor V Leiden mutation (one homozygote, 2 heterozygote), while 7 of 39 (17.9%) patients with no thrombotic history had the factor V Leiden mutation (2 homozygotes, 5 heterozygotes). There is no statistical difference in the frequency of the factor V mutation between patients with BD with no thrombosis and the control group. The frequency of thrombosis in BD with and without factor V Leiden mutation was (3/10) 30% and (2/34) 5.9%, respectively. These findings suggest that homozygosity or heterozygosity for factor V Leiden is not always associated with occurrence of venous thrombosis in BD, but it may be a contributing risk factor for venous thromboembolic events in these patients.