Common mutations in three genes (MTHFR 677 C-T; MS 2756 A-G; CBS Exon 8,844 ins 68) in homocysteine metabolism have been shown to cause increased plasma homocysteine levels thus causing a predisposition to thrombosis. FV 1691 G-A mutation, which is very common in the Turkish population, was also studied. As there is no existing data in the Turkish population, we aimed to study these mutations in patients with thrombosis and normal controls. The case-control study included 52 patients with the diagnosis of deep vein thrombosis (DVT) and 106 controls, consecutively selected among subjects without personal and family history of atherothrombosis. Patients with DVT were selected if Doppler ultrasonography was positive. The comparison of FV 1691 G-A mutation revealed statistically significant difference in control and DVT group. Risk assessment of double prothrombotic gene alterations indicated only FV 1691 G-A mutation as an independent risk factor for thrombosis, but our data suggested that MTHFR 677 has little effect on its own but may have synergy with FV 1691 G-A. Other possible risk genotypes at the homocysteine pathway did not have a significant effect on thrombosis. Furthermore, being heterozygote at two different loci or homozygosity at least in one locus also did not reveal a significant difference between these two groups in our population.