Thrombophilia may be defined as an acquired or congenital abnormality of hemostasis predisposing to thrombosis. Some of the inherited abnormalities such as factor V Leiden mutation, factor II G20210A mutation as well as deficiencies in antithrombin, protein C and protein S, are already known to be risk factors for venous thromboembolism. This review focuses on the link between these abnormalities and arterial thrombosis. Routine screening for these disorders is not indicated in most cases of arterial complications, but could be useful in some sub-groups of patients, such as young patients, smokers, patients on oral contraception, or those with premature occlusion after revascularization procedures. Anticoagulation rather than antiplatelet therapy may be preferable for these patients.