We investigated the effect of antithrombin III on 60 min warm intestinal ischemia-reperfusion (IR) injury in rats. Sprague-Dawley rats, weighing 220-250 g, were divided into three groups: group 1 sham-operated group (no IR injury, n=8), group 2 ischemic control group (control, Ringer's lactate infused, n=8), group 3 Antithrombin III treated group (2.50 U/kg before ischemia, n=8). Intestinal ischemia was induced in rats by occluding the superior mesenteric artery for 60 min. Malondialdehyde (MDA) levels, myeloperoxidase activity (MPO) and mucosal damage were investigated after 120 min reperfusion. Elevated MDA levels and MPO activity and severe histopathological damage were observed in the control group compared with the sham group (P<0.05). Decreased MDA levels and MPO activity and less histopathological damage were detected in group 3 compared with the control group (P<0.05). Accumulation of lipid peroxidation products and neutrophils in mucosal tissues were significantly inhibited by antithrombin III treatment. We conclude that treatment with antithrombin III before intestinal ischemia prevents histological damage in rats.