Venous thromboembolism (VTE), including deep venous thrombosis (DVT) and pulmonary embolism (PE), occurs secondary to a number of hereditary and acquired disorders of hemostasis. A recently recognized polymorphism in Factor V (FV) gene H1299R (also named HR2) has been reported to be a possible risk factor for the development of VTE. The aim of this study is to evaluate the role of HR2 polymorphism in VTE in a group of Lebanese patients. Seventy-three VTE patients and 125 healthy subjects were examined for HR2. The average ages for the patients and controls were 45.0+/-19.1 years and 35.4+/-18.6 years, respectively. Sixty patients (82.2%) had DVT, eight patients (11%) had PE, and five patients (6.8%) had both. There was significant association between FV Leiden and VTE (p<0.001). HR2 haplotype had a prevalence of 16.4% in patients. VTE patients with normal FV were 2.7 times more likely to have the HR2 haplotype as compared to controls with normal FV (p=0.036, 95% CI=1.04-7.06). We conclude that the FV HR2 haplotype significantly affects the risk of VTE in subjects with normal FV. This finding entails that screening for the HR2 haplotype should be done in VTE patients with normal FV Leiden results.