Behcet's disease is a chronic systemic vasculitis with particular systemic features including thrombotic events. The present study was designed to analyse the role of the factor V Leiden and the prothrombin G20210A mutations and plasminogen activator inhibitor-1 4G/5G polymorphism on the thrombotic risk of patients with Behcet's disease. A total of 50 unrelated patients with Behcet's disease (34 male, 16 female) were the subjects of the study. Twenty-seven of 50 patients with a history of thrombosis comprised group 1, and 23 patients with no thrombosis comprised group 2. In group 1, nine of the 27 patients (33%) were found to have the factor V Leiden mutation (7.1% in healthy population), and the 4G/4G genotype was found in 23% of the patients (26% in control). No patient had the prothrombin G20210A mutation (2.2% in healthy control). In group 2, two patients (9%) had the factor V Leiden and one patient (4%) had the prothrombin G20210A mutations. The 4G/4G polymorphism was found in 30.5% of the patients. The differences in the frequencies of factor V Leiden mutation between group 1 and group 2 (odds ratio, 5.3; 95% confidence interval, 1.0–27.5) and between group 1 and the healthy population were statistically significant (P < 0.05). No statistically significant association was found for the prothrombin G20210A mutation and the 4G/5G genotype between the two groups or between each group and the healthy population, indicating that the prothrombin G20210A mutation and the 4G/4G polymorphism do not play a role in the development of thrombosis in Behcet's disease. These data suggested that the factor V Leiden mutation might be a risk factor for the development of thrombosis in Behcet's disease patients.