In this study, we evaluated common inherited thrombophilic risk factors in patients with antiphospholipid syndrome (APS), and reviewed relevant literature. Ninety-four APS patients with documented thrombosis, 40 patients with persistent antiphospholipid antibody (aPLA) positivity but without thrombosis, and healthy controls were screened. We found that inherited protein C, protein S, and antithrombin deficiencies were rare in APS patients. The presence of factor V Leiden G506A (FVL) mutation was significantly higher in APS patients with thrombosis compared to healthy controls (11.2% versus 4.9%, P = 0.0043). The prevalence of prothrombin G20210A mutation, however was not significantly increased in APS patients with thrombosis compared to patients without thrombosis (2.7% versus 1.25%, P = 0.67). Our literature review suggested that FVL mutation was associated with both arterial and venous thrombosis but prothrombin G20210A mutation does not seem to contribute much to thrombotic risk in patients with APS. In conclusion, the presence of FVL mutation may define a small but important subgroup of patients who had high risk of both venous and arterial thrombosis. Known thrombophilic risk factors however, may influence the development of thrombotic complications in approximately 10% of APS patients. These findings may indicate that thrombotic complications in APS patients are largely related with aPLA-mediated mechanisms.