A 28-year-old man admitted to our hospital because of severe neck pain, headache, fever and vomiting. He was alert and had no neurological deficit except for nuchal stiffness. Cerebrospinal fluid (CSF) examination showed elevated mononuclear cell counts (68/mm(3)) and protein levels (300 mg/dl). He was diagnosed as having aseptic meningitis and was thereby treated. Two days later, he manifested seizure and on the next day, severe cerebral hemorrhage occurred in the left parietal lobe and decompression surgery was performed. Cerebral venous thrombosis was strongly indicated by operative findings, cerebral angiography and retrospective assessment of MRI images. Genetic testing revealed a novel mutation (p.Cys449Tyr) combined by Protein S Tokushima mutation (p.Lys196Glu) which is frequently observed in Japanese. Possibility of CVT should be noted, even when a patient exhibits clinical symptoms and CSF findings compatible with a diagnosis of aseptic meningitis.