BACKGROUND: Moderate hyperhomocysteinemia and factor V Leiden mutation are among the most prevalent risk factors for venous thromboembolism (VTE). The hypothesis of an interaction between those risks has been raised and conflicting results were reported. METHODS: We designed a hospital-based case-control study to test the interaction between Factor V Leiden and fasting serum total homocysteine (tHcy). We have also analysed the G20210A prothrombin gene variant. This study enrolled 904 hospitalised patients who had an objectively proven deep vein thrombosis and/or pulmonary embolism as well as 904 hospitalised control patients matched for gender, age and major acquired risk factor for VTE. RESULTS: Our data did not detect any multiplicative interaction between hyperhomocysteinemia (>15 mumol/L) and factor V Leiden mutation or G20210A prothrombin gene variant. Odds ratios (95% CI) were 4.0 (1.5-11) and 6.0 (1.3-27) for the combined effect of hyperhomocysteinemia with either factor V Leiden mutation or G20210A prothrombin gene variant, respectively. CONCLUSIONS: Current data provide further knowledge in relationship between hyperhomocysteinemia and inherited risk factors, such as factor V Leiden mutation and G20210A prothrombin gene variant. As those risk factors are not so rare among Caucasians, a better estimate of the risk related to double exposure might help to optimise venous thromboembolism prevention.