The contribution of mutations in the prothrombin (FII G20210A), methylenetetrahydrofolate reductase (C677T) genes and factor V Leiden (FVL) to the pathogenesis of arterial thrombosis remains controversial. In this study, these polymorphisms were investigated by polymerase chain reaction-restriction fragment length polymorphism in a group of 53 patients that presented arterial thrombosis other than myocardial infarction as a first thrombotic event and 275 control subjects living in the state of Minas Gerais, Brazil. Odds ratio (OR) and chi tests were applied for statistical comparisons. Similar frequencies were detected among patients and control subjects for the C677T mutation. The 20210A mutation was present in 3.6% of the control subjects but was not detected among ischemic stroke patients. Significant differences were detected only for factor V Leiden (odds ratio 7.11; 95% confidence interval 1.55-32.73). Our data indicate that, among these genetic factors, factor V Leiden was identified as an important risk factor for arterial thrombosis in this group of patients. In addition, our results indicate regional differences in the incidence of these genetic factors in Brazil, as compared to the incidences reported in other studies.