Recent studies have demonstrated association between ABO blood system and thrombosis, indicating that individuals belonging to non-O blood groups (A, B or AB) present an increased risk of venous thrombosis, heart disease, and ischemic stroke (IS) as compared to O blood group carriers. In this study, we investigated the frequency of ABO blood group polymorphisms and its association with IS and peripheral arterial disease. Significant differences were observed for O1 (OR 0.57, 95% CI 0.35-0.95, p < 0.05) and O2 (OR 3.47, 95% CI 1.15-10.28, p < 0.05) alleles among IS patients while significant differences were observed for B phenotype (26.3 vs 9.5%, OR 3.42, 95% CI 1.32-8.76, p = 0.01, patients vs controls, respectively) and alleles A1 (OR 0.31, 95% CI 0.11-0.84, p < 0.05), O2 (OR 4.61, 95% CI 1.59-13.23, p < 0.01) and B (OR 3.42, 95% CI 1.62-7.13, p < 0.001) alleles for PAD patients. O1 allele was an independent variable (OR 0.27, 95% CI 0.12-0.57, p < 0.001) for IS patients. These data suggest the relationship of non-O blood groups in pathogenesis of thrombosis events and a possible protective effect of O blood group.