The clinical symptoms, causative factors, and prognosis in Japanese patients with cerebral venous thrombosis have not been adequately characterized. The present study describes these features in patients in Japan. Twenty-two patients with cerebral venous thrombosis were retrospectively identified. Diagnosis was confirmed by either digital subtraction angiography, magnetic resonance venography, or contrast-enhanced computed tomography. Demographic data and clinical and radiological features were recorded and analyzed for each patient. Prognosis was evaluated by the modified Rankin scale (mRS) at the time of hospital discharge. The most frequent symptom of cerebral venous thrombosis was headache (59.1 %). Causative factors included congenital thrombophilia (31.8 %), acquired thrombophilia (27.3 %), and iron-deficiency anemia (13.6 %). Of seven patients with congenital thrombophilia, four had mutations in the protein S gene, two had mutations in the protein C gene, and one had mutations in the antithrombin gene. All patients were alive at discharge from hospital. Nineteen of the 22 patients (86.4 %) recovered completely or exhibited only mild residual symptoms (mRS 0-2). However, three patients (13.6 %) had a poor prognosis (mRS 3-5). Cerebral venous thrombosis in Japanese patients is frequently associated with congenital thrombophilia and protein S gene mutation.