The traditional, retrocolic/antegastric Roux-en-Y choledochojejunostomy is technically complicated, and the incidence of postoperative complications remains high. Here we report the outcome of 59 consecutively treated patients (study group, SG) that underwent a new choledochojejunostomy method in which the jejunal loop is passed behind the antrum pyloricum (retrogastric route). A retrospective comparison was made between this group of patients and 187 patients (control group, CG) that underwent conventional Roux-en-Y choledochojejunostomy (antegastric route). Baseline clinicopathological characteristics were similar in both groups, except for the BMI, which was significantly higher in the SG. The time spent on constructing the anastomosis, as well as overall postoperative complications, did not differ between groups. Compared with the CG, the incidence of postoperative delayed gastric emptying was decreased in the SG, and the time elapsed before the patients’ first postoperative liquid food consumption was shorter. We ascribe these beneficial effects to the superiority of the modified, retropyloric choledochojejunostomy approach, and propose that this surgical technique is particularly suitable for obese patients, especially those with a short ascending bowel loop.