We describe four pediatric patients with ulcerative colitis and cerebral sinovenous thrombosis and review the pediatric and adult literature on the treatment of sinovenous thrombosis. All of our patients had headache as the initial complaint with onset during an ulcerative colitis flare. Evaluation for hypercoagulable states revealed heterozygosity for prothrombin gene mutation and increased homocysteine level in one patient and mild elevation of anticardiolipin antibodies in two patients. Treatment in the acute period included thrombolysis, heparin, and low-molecular-weight heparin. Chronic therapy included warfarin, low-molecular-weight heparin, and aspirin. Peripheral vein thrombosis occurred in two patients while not on antiplatelet or anticoagulation therapy. Neurologic outcome was positive in this series without complications of therapy, suggesting that aggressive therapy should be considered. Although anticoagulation therapy of sinovenous thrombosis is controversial, particularly in the context of intestinal hemorrhage, it can be beneficial given the possibility of an ongoing hypercoagulable state.