The risk of thromboembolism is increased in inflammatory bowel disease and its symptoms may be overlooked. Furthermore, its treatment can be complex and is not without complications. We describe a case of an adolescent boy who developed a cerebral sinus venous thrombosis during a relapse of his ulcerative colitis and who, while on treatment with heparin,developed heparin-induced thrombocytopenia (HIT).The treatment was then switched to fondaparinux, a synthetic and selective inhibitor of activated factor x.