Objectives: A precipitating factor for marginal ulcer formation after Roux-en-Y gastric bypass may be the prolonged irritation by foreign material, such as nonabsorbable suture at the gastrojejunostomy. This study examines the incidence of marginal ulcers before and after a change was made from using nonabsorbable suture to using absorbable suture for the inner layer of the anastomosis. Methods: A total of 3285 laparoscopic Roux-en-Y gastric bypass operations were performed during a 5-year period. The gastrojejunostomy technique was modified in August 2002. Those patients who developed a marginal ulcer postoperatively were identified, and their charts were retrospectively analyzed for the operative technique, patient age, history of previous gastric surgery, presence of preoperative diabetes, coronary artery disease, or peptic ulcer disease, and use of nonsteroidal anti-inflammatory medications or tobacco. Results: The incidence of marginal ulceration after Roux-en-Y gastric bypass decreased significantly from 2.6% (28/1095) with the use of nonabsorbable suture to 1.3% (29/2190) after the change to absorbable suture for the inner layer of the gastrojejunal anastomosis (P < .001). The incidence of visible suture adjacent to the ulcer on endoscopy was also significantly reduced (64.3% vs 3.4%; P < .001). When the results were corrected for length of follow-up, the difference in the incidence of ulcers occurring within 1 year of surgery remained significant between the two groups (P = .002). There were no other significant differences in the factors analyzed. Conclusions: The use of nonabsorbable sutures for the inner layer of the gastrojejunal anastomosis is associated with an increased incidence of marginal ulcers, and the adoption of absorbable suture material has reduced this incidence.