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Background: Long-term results of Roux-en-Y gastric bypass (RYGB) are nonexistent in the veterans affairs (VA) population. We compare excess weight loss (EWL) success and medical comorbidity changes between the VA and non-VA population after RYGB., Methods: Retrospective review of consecutive subjects undergoing RYGB from 1997 to 2002 at the Los Angeles VA. Weight and comorbidity data were collected every 6 and 12 months, respectively., Results: Fifty-nine subjects were included; 54%, 58%, 46.8%, and 44.1% of subjects achieved EWL >50% at years 1 to 4. Hypertension resolved in 23%, 30%, and 32% at months 12 to 36. Obstructive sleep apnea resolved in 37%, 48%, 48%, 44%, and 60% at months 12 to 60. Diabetes mellitus resolved in 86%, 84%, 79%, and 80% at months 12 to 48. Improvements in the lipid panel were observed by month 12 and maintained thereafter., Conclusions: EWL and proportion of subjects with resolved hypertension and obstructive sleep apnea are inferior to the non-VA population. Nevertheless, improvements in measures of success are maintained in the VA population.