Cerebral venous thrombosis (CVT) has been associated with thrombophilic defects. We performed a study to evaluate the role of three single nucleotide polymorphisms (SNP), factor V Leiden G1691A (FVL), prothrombin gene mutation G20210A (FII-G20210A) and methylenotetrahydrofolate reductase variant C677T (MTHFR-C677T), as risk factors for CVT in Tunisian patients. A single center case-control study (26 patients with CVT and 197 controls) was performed. Genomic DNA was tested for the three SNP. The principle finding was the association between FVL and CVT (p<0.001, Odds ratio=6.1, 95% confidence interval=2.3–16.5). However, neither the FII-G20210 (p=0.536) nor the homozygous MTHFR-C677T genotype (p=0.325) variant contributed to the risk of CVT in these Tunisian patients.