SummaryBackground: Ulcers at the gastrojejunostomy site are a common problem after gastric surgery. Their postoperative development seems to be associated with Helicobacter pylori-related gastritis or abuse of nicotine, alcohol or non-steroidal anti-inflammatory drugs (NSAIDs), but is also dependent on the choice of surgical method (Roux-en-Y or B-II gastric bypass). Patients and Methods: This study evaluated the follow-up of 1,908 patients over a period of 5 years (January 2006 to December 2010). In 1,861 cases, we performed a Roux-en-Y gastric bypass, and in 47 cases a B-II gastric bypass. Results: All patients (n = 407) with symptoms such as dysphagia, reflux, nausea, vomiting or epigastric pain underwent gastroscopy. In 52 cases, ulcers were found at the gastrojejunostomy site. Of these patients, 39 (75%; p < 0.0001) had consumed alcohol, nicotine or NSAIDs; in 14 patients (27%; p < 0.0001) we detected H. pylori-related gastritis. A total of 2.4% of the patients after Roux-en-Y gastric bypass (45/1,861) and 14.9% of the patients after B-II gastric bypass (7/47) developed ulcers at the gastroenteral junction. The difference is clearly significant (Fisher's exact test, p = 0.0002). Furthermore, there were signi ficant differences regarding the recurrence rate: 86% of the B-II gastric bypass group and 13.3% of the Roux-en-Y gastric bypass group needed to be treated several times. Conclusions: Every patient needs to be informed preoperatively that there is a markedly increased risk of ulcers at the gastroenteral junction, particularly if the patient cannot avoid potential risk factors (nicotine, alcohol, NSAIDs). Preoperative gastroscopy with H. pylori testing and subsequent eradication can also reduce the risk of ulcers. An increased incidence of peptic ulcers after B-II gastric bypass was noted. All of these patients were converted to Roux-en-Y.