Background: This study investigates the association between cerebral vein thrombosis (CVT) and the mutations FV 1691A (factor V Leiden), PT 20210A and MTHFR 677TT and acquired factors including oral contraceptive (OC) use. Methods: 26 patients (21 females) and 217 healthy controls (134 females) were studied. Multiple regression analysis was performed. Results: The frequency of the three mutations in cases and controls were: PT 20210A, 23 versus 1%, odds ratio (OR) 21.40 (95% CI 4.29–118.75), p < 0.001; FV 1691A, 8 versus 1%, OR 5.94 (95% CI 0.66–46.9); MTHFR 677TT, 4 versus 7%, OR 0.54 (95% CI 0.03–4.08). OC use was more frequent in female patients over 14 years old than in controls (84 vs. 40%, OR 8.15, 95% CI 2.09–37.13, p < 0.001). The model that best explained the thrombotic risk included PT 20210A and OC use. Conclusions: PT 20210A and OC use are the main thrombophilic risk factors predisposing to CVT and should be routinely investigated in patients with this disease.