Gastric bypass procedures have been used widely in the surgical therapy of morbid obesity. Evidence exists that the bypassed gastric segment retains its ability to secrete acid. Acid-related ulceration and obstruction of the proximal gastric pouch after surgery have been well documented, but duodenal ulceration after gastric bypass has yet to be reported. We present the first reported case of duodenal ulceration and perforation after gastric bypass surgery for morbid obesity. This case demonstrates that acid-related gastroduodenal disease may occur in the bypassed gastrointestinal tract. Consideration should be given to this area in evaluating upper gastrointestinal bleeding and abdominal pain after gastric bypass. Because barium contrast studies may not adequately evaluate bypassed segments, and standard gastroscopes are not long enough to reach these areas, the use of longer endoscopes may be necessary to confirm the presence of gastroduodenal disease after gastric bypass.