Background Bariatric surgery remains the most effective treatment for morbid obesity, and laparoscopic Roux-en-Y gastric bypass (LRYGB) continues to be the preferred operation. However, data for long-term outcomes are lacking. Our goal was to determine the long-term clinical outcomes after LRYGB. Methods Retrospective review of a prospectively maintained database was conducted on all patients who underwent LRYGB from 2001-2006. Only patients who had postoperative clinic visits both at <= 2 and >= 5 years were included. Data collected included patient demographics and postoperative clinical outcomes, including percent excess weight loss (%EWL), complications, and improvement or resolution of preoperative comorbidities (type 2 diabetes mellitus, hypertension, obstructive sleep apnea, and hyperlipidemia). Data were analyzed by using SAS (version 9.2) and SPSS (version 16) statistical software. Results There were 770 patients who underwent LRYGB at UAB from 2001-2006. Of these, 172 patients met inclusion criteria (148 women and 24 men) with a median age of 41 years and median body mass index of 46 kg/m(2). Median short- and long-term follow-up was 12 and 75 months, respectively. Mean %EWL was 69 % for short-term and 65 % for long-term follow-up (P = 0.0032). Of 172 patients, 66 experienced 81 complications at a median of 26 months after operation. The improvement or resolution of comorbidities was maintained in the long-term, and there was no statistically significant difference compared with improvement or resolution in the short-term. Conclusions Although there was a statistically significant difference in %EWL between short- and long-term follow-up, both arms showed a clinically relevant %EWL (69 and 65 %) and both were statistically significant compared with preoperative values. The improvement or resolution of comorbidities achieved with LRYGB was maintained in long-term follow-up. Thus, LRYGB resulted in significant improvement in clinical outcomes that were durable in the long term.