A 47-year-old male receiving anticoagulant therapy for thrombophlebitis in the left leg for several years presented with mild left hemiparesis and ipsilateral hypesthesia. The cause of the thrombophlebitis was still unknown. Magnetic resonance (MR) imaging showed subacute thrombosis of both the superior sagittal sinus (SSS) and a cortical vein in the right cerebral hemisphere. Fluid attenuation inversion recovery axial MR imaging demonstrated these lesions more obviously than conventional T2-weighted axial MR imaging. Right carotid angiography showed a partial SSS filling defect and occlusion of the cortical vein with collateral circulation. Coagulation studies revealed decreases in both protein C activity and antigen levels with normal levels of blood coagulation factors II, VII, IX, and X and protein S activity and antigen. The patient's mother had normal levels of both protein C activity and antigen, but his father had decreased levels. The diagnosis was SSS and cerebral cortical venous thrombosis caused by congenital protein C deficiency. The patient was treated conservatively, and his clinical course was uneventful. His neurological dysfunctions recovered within approximately 3 weeks after the onset. Ten months later, right carotid angiography showed recanalization of the SSS and partial filling of the cortical vein. Anticoagulant therapy has been continued, and no cerebral venous thrombosis has recurred during the 1.5 years after the onset.