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Venous and arterial thromboembolism constitutes a significant cause of morbidity and mortality in patients with inflammatory bowel disease. The most common thrombotic manifestations are lower extremity deep vein thromboses with or without pulmonary embolism. Occasionally, thromboembolic events occur in the main abdominal vessels, such as the portal and superior mesenteric veins, vena cava and hepatic vein, aorta, splanchnic and iliac arteries, or in the limb arteries. The decision-making process for the treatment of these uncommon thromboembolic complications in inflammatory bowel disease may be very challenging for several reasons: 1) no standardized therapies are available; 2) the decision of starting anticoagulant therapy implies the potential risk of intestinal bleeding; 3) thromboembolic events may recur and be life-threatening if inadequately treated. The literature was searched by using MEDLINE, Embase, and the Cochrane library database. Studies published between 1970 and 2007 were reviewed. We discuss the medical and surgical therapeutic options that should be considered to optimize the outcome and reduce the risk of complications in abdominal thromboembolisms associated with inflammatory bowel disease.