Ulcerative colitis (UC) can be complicated by various extra-intestinal manifestations such as thromboembolic disease. Most thrombotic events occure in lower extremities, whereas the incidence of cerebral venous involvement is very rare and serious in children. We present a case of a nine years old boy with UC and cerebral venous thrombosis diagnosed at the same time. A nine years old boy with a 3-week history of bloody diarrhea and abdominal pain was admitted to our hospital. On admission his laboratory data showed anemia, leukocytosis, thrombocytosis and elevated erythrocyte sedimentation rate. Colonoscopic evaluation revealed severe active pancolitis with diffuse ulceration. The day after colonoscopy he had complained of severe headache. Neurolological examination revealed pitosis of the left palpebra and bilateral papilledema. Magnetic resonance (MR) imaging and MR venography revealed thrombosis in the left transvers sinus and sigmoid sinus. The patient was treated immediatly with heparin. At the same time he was diagnosed with severe active UC based upon histopathological findings and managed initially with mesalamin and prednisolon. He also had been screened for thrombophilia. Protein C, protein S, antithrombin III, factor VIII, homocystein, prothrombin II and fibrinogen levels were in the normal range but he was heterozygous for the methylene tetrahydrofolate reductase gene mutation. After two weeks of therapy his bloody diarrhea was controlled, headache and neurolological findings were improved. His treatment was continued with mesalamin, prednisolon, azathioprin and low molecular weight heparin, but repeated MRI and MRI venography showed neither extension nor improvement of the thrombosis.