Background: Intestinal obstruction occurs in 2-3% of patients following Roux-en-Y gastric bypass (RYGB) surgery; many of these are due to Petersen’s internal hernia. There is controversy as to whether the alimentary limb should be placed in the retro-colic or ante-colic position to reduce this incidence. Methods: A retrospective analysis was performed on 444 patients undergoing RYGB surgery for morbid obesity during a six year period. During operation, the surgeon chose the positioning of the 75 cm alimentary limb based upon technical consideration. Group A (216) patients had placement of the Roux limb anterior to the transverse colon and group B (228) patients had placement of the limb through an opening created in the transverse mesocolon. The average age was 40 years (range 19-64) and the body mass index BMI ranged from 40-75 kg/m2. Patients were followed for 14 - 80 months (mean 30 months). Any patient lost to follow-up was excluded. Results: Group A had 16 patients (7.4%) that had early intolerance to enteral intake, compared to 13 patients in group B (5.7%, p > 0.05). 13 patients required re-operation for intestinal obstruction (7 patients in group A and 6 patients in group B (p > 0.05). None of the intestinal obstructions in group A were due to Petersen’s hernia whereas this was the etiology in four of the six patients in group B. The development of anastomotic stricture was 1 patient (0.5%) in group A and 3 patients (1%, p > 0.05) in group B. No other complications during the follow-up period were attributed to the position of the alimentary limb. Conclusion: Placement of the Roux limb in the antecolic position is technically easier in some patients and does not appear to be associated with more complications than a retrocolic alimentary limb. It avoids the risk of an internal hernia through the transverse mesocolon but does not appear to reduce the incidence of intestinal obstruction or feeding difficulties either in the early or late post-operative period.