OBJECTIVE Vasculitis is one of the major findings of Behçet's disease (BD). Protein Z (PZ) is a glycoprotein that acts as a cofactor of PZ-dependent protease inhibitor and suppresses trombus formation by inhibiting activated factor Xa. Polymorphism of the PZ gene was mentioned as a genetic risk factor for various thrombotic events. The aim of this study is to investigate the intron F G79A polymorphism of the PZ gene in Behçet patients with and without ocular involvement. METHODS Seventy-six patients and 70 controls were included in the study. Intron F G79A polymorphism of PZ gene was determined by polymerase chain reaction based DNA analysis. The frequency of A allele and the distribution of genotypes were assessed by χ(2) test and the genotype distribution and Hardy-Weinberg equilibrium were tested with the χ(2) test for quality of fit. RESULTS The frequency of the A allele was significantly higher in overall Behçet patients than in controls (odds ratio [OR] = 6.8; 95% CI, 2.6 to 17.9; p = 0.0001). It was also significantly higher in patients with (OR = 5.3; 95% CI, 1.83 to 15.6; p = 0.0024) or without (OR = 8.2; 95% CI, 2.95 to 22.5; p = 0.0001) ocular involvement compared to controls. However, A allele frequency was not significantly different between patients with eye involvement versus patients without eye involvement (OR = 0.65; 95% CI, 0.3 to 1.4; p = 0.28). CONCLUSIONS Although thrombosis in BD is multifactorial, intron F G79A polymorphism of PZ gene in BD may be one of the factors that contribute to this pathological process.