This report describes the second case of a superior mesenteric and portal vein thrombosis following an uneventful laparoscopic Nissen fundoplication. The patient presented on postoperative day 10 with acute onset of abdominal pain and inability to tolerate oral food. A computed tomography (CT) scan revealed superior mesenteric and portal venous thrombosis with questionable viability of the proximal small bowel. He was heparinized and taken for emergent exploratory laparotomy. At surgery and at a planned re-exploration the following day, the bowel was viable and no resection was needed. Despite continuation on anticoagulation therapy, he developed a pulmonary embolism. A hypercoagulable workup was normal. After continued anticoagulation therapy and supportive care, a duplex ultrasound 2 months after the event showed normal flow in both the superior mesenteric and portal veins. Possible mechanisms are discussed along with a review of the pertinent literature.