Objective: The current case-control study was aimed to determine the prevalence and the clinical significance of inherited thrombophilia - factor V Leiden and G20210A prothrombin polymorphisms - in patients with antiphospholipid syndrome (APS).Methods: 100 patients with APS (77 with primary APS and 23 with systemic lupus erythematosus [SLE]-APS), and 100 patients with first lower extremity deep venous thrombosis (DVT), and 200 healthy individuals as a control groups were analysed. Patients and control group were tested for factor V Leiden and prothrombin G20210A gene polymorphism.Results: Factor V Leiden variant was found in 1% of APS patients, in 3% of healthy individuals (p=0.49), and 16% of patients with first DVT (p<0.0005). Prothrombin gene polymorphism was found in 6% of APS patients and in 2.5% of healthy subjects (p=0.21), and 13% of patients with DVT (p=0.14). In primary APS patients, factor V Leiden was present in 1.3% (1/77) and prothrombin gene polymorphism in 6.5% (5/77). No patient with SLE-APS had factor V Leiden and prothrombin gene variant was present in only one patient (4.3%). Patients with prothrombin polymorphism had higher prevalence of venous thrombosis, with no statistical significance (80% vs. 47.9%, p=0.35). There were no differences in the prevalence of recurrent thrombosis before or after APS diagnosis in patients with or without prothrombin gene polymorphism.Conclusion Factor: V Leiden and G20210A prothrombin variant seem to play no role in either the development of APS or in the type of involved vessel, with no increased risk of re-thrombosis during follow-up. © Clinical and Experimental Rheumatology 2013.