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Background Emphasis on the development of designated programs for bariatric surgery as a method of quality improvement has increased; however, the data on the effect of these programs on the clinical outcome are insufficient. The aim of the present study was to consider the effect of the implementation of a bariatric clinical program on patient outcomes in a high-volume academic setting. Methods We implemented a focused bariatric clinical program to establish common clinical pathways and improve the critical clinical processes. To evaluate the effect of this program, we studied outcome and quality indicators, such as caseload, average length of stay (ALOS), and mortality, readmission, and complication rates during the 6-year period since the introduction of the program. Results From June 2000 to June 2006 (financial year 2001–2006), 1886 Roux-en-Y gastric bypass procedures were performed at our institution, with 7 deaths (.37%). During this period, we observed a progressive decrease in the ALOS from 6.7 days in 2001 to 3.2 days in 2006, a significant reduction of the 30-day readmission rates from 15.7% in 2001 to 8.1% in 2006, and a reduction of the observed overall complication rate from 18.6% in 2001 to 4.8% in 2006. Conclusion We observed a significant improvement in patient outcomes with the introduction of a designated bariatric surgery program. Additional studies of the validity of these quality indicators are needed to determine the true effect of these quality improvement programs.