We present a case of the multiple venous intestinal infarction in patient with two inherited thrombophilias: Leiden factor V (LFV) and factor VIII elevation. The patient had a critical hypocoagulation caused by vitamin K antagonist (VKA) overdose. At laparotomy, several intestinal segments were necrotic and ischemic. Coagulopathy was corrected by the transfusion of the fresh frozen plasma. Because of the 4th duodenal segment infarction distal segmental duodenectomy with side-to-side duodenojejunostomy was done, which is a rarely performed procedure. On postoperative day 6 deep vein thrombosis developed, despite nadroparin profillaxes, early mobilisation and compressive stockings. Our case demonstrated that in patients with congenital thrombophilia, development of the mesenteric venous thrombosis is possible even with VKA induced severe hypocoagulation. Venous infarction of the small bowel can be associated with the hemoperitoneum and gastrointestinal bleeding. After resection of the fourth duodenal segment, side-to-side duodenojejunostomy is a feasible method of reconstruction.