BACKGROUND: Cerebral venous thrombosis (CVT) is a rare disease and it has different etiologies. Inherited or acquired prothrombotic state plays a key role in the development of CVT.METHODS: A 28-year-old man who presented to our emergency department with persistent headache and accompanied by complaints of nausea and vomiting over a week. Neurologic examination revealed bilateral papilledema. Brain computed tomography showed a hyperdense area on the posterior part of the occipital lobe. Brain magnetic resonance imaging and magnetic resonance venography revealed thrombosis of CVT. Homozygous mutations were found for methylenetetrahydrofolate reductase (MTHFR). MTHFR CG677T gene mutation and blood tests showed elevated homocysteine levels on the etiological screening. There was no other etiology for CVT.RESULTS: Headache and other complaints were improved after treatment of heparin, warfarin, and vitamin B12. No recurrence of symptoms was observed upon outpatient follow-up.CONCLUSION: Since CVT is an important cause of headache, we recommend etiology screening for patients who present with CVT for MTHFR gene mutations and family counseling should be provided.