Background: Marginal ulceration (MU) is a recognized complication of Roux-en-Y gastric bypass (RYGB) surgery. While several possible risk factors have been reported, the mechanism of MU remains incompletely understood. The aim of this study was to compare the effect of surgical technique on the incidence of MU. Methods and Material: This was a retrospective study of 749 patients undergoing RYGB over a ten-year period with at least one year of follow-up. The diagnosis of MU was made based on clinical symptoms and confirmed by postoperative endoscopy (POE). We assessed four different gastric bypass (GBP) techniques: T1-Open, non-divided stomach, circular stapler, non-vagotomy (n = 332); T2-Open, divided stomach, circular stapler, vagotomy (n = 91); T3-Laparoscopic, divided, circular stapler, vagotomy (n = 152); T4-Laparoscopic, divided, linear stapler, vagotomy (n = 174). Results: The four groups were similar with respect to age and mean BMI. The frequency of POE was 16%, 25%, 28% and 27% in groups T1-T4 respectively (NS). The incidence of MU was significantly lower in T1 (2.1%) compared to T2 (5.5%), T3 (15.1%) and T4 (12.6%), p < 0.05. MU occurred significantly more frequently with an antecolic Roux limb versus retrocolic (14.5% vs 5.6%, p < 0.05). Conclusion: The incidence of MU after RYGB surgery is influenced by surgical technique. The lowest incidence of MU was with a non-divided stomach, no vagotomy, transverse staple line, and circular stapled anastomosis. A retrocolic Roux limb was protective. There was no difference in the incidence of MU using laparoscopic versus open bypass if a similar technique was employed or using linear versus circular stapler for the gastrojejunostomy.