Background Application of the robot for Roux-en-Y gastric bypass has been slow to evolve, despite its rapid acceptance in other fields. This is largely due to associated costs of technology, reports of increased operative time, and inadequate data available to correlate the benefits of robotics to a clinical outcome. The authors present a comparative study between laparoscopic and robot-assisted Roux-en-Y gastric bypass performed at a specialized institution for robotic surgery. Materials and method A total of 135 consecutive Rouxen-Y gastric bypass procedures were performed from January 2006 to December 2009 by a single surgeon. The first 45 were performed laparoscopically and the remaining 90 were robot-assisted. Patient demographics, operative time, complication rate, length of stay, long-term weight loss, and follow-up for the two groups were gathered from a prospectively maintained database and statistically analyzed. Results The overall operative time was significantly shorter for the robot-assisted procedures than for the laparoscopic procedures (207 ± 31 vs. 227 ± 31 min) (P = 0.0006). The robotic set-up time remained constant at 13 ± 4 min. 30 robotic cases were necessary in order to perform the procedure in less time than with the laparoscopic approach (P = 0.047). Mortality was 0% in both groups, with no conversions to open surgery and no transfusions. Early morbidities and percentage of excess weight loss at 1 year were comparable for the two groups. Conclusions The use of the robot for performing the gastrojejunostomy during laparoscopic Roux-en-Y gastric bypass does not increase the operative time or the rate of specific complications. The short-term outcomes of the robot-assisted procedure are comparable to those found with the conventional laparoscopic method.