We report the case of a 40-year-old man with a perforated duodenal ulcer who underwent antrectomy at laparotomy, and in whom standard truncal vagotomy was not technically possible due to an intraabdominal abscess. Thoracoscopic truncal vagotomy performed at the level of the inferior pulmonary vein was successful in completely eliminating symptoms due to peptic ulcer disease without producing clinically significant morbidity. The minimal morbidity and short hospital stay suggest that thoracoscopic truncal vagotomy provides a reasonable alternative in patients with complicated intraabdominal abscesses due to peptic ulcer disease.