Introduction: Laparoscopic Roux-en-Y gastric bypass (LRYGB) has been advocated as definitive therapy for GERD in morbidly obese patients. This study evaluates the physiology of the gastric pouch after LRYGB. Methods: We evaluated patients who underwent laparoscopic RYGB for morbid obesity within the period 01/99 to 12/01 and identified those patients who presented with GERD as a co-morbid factor. Only patients with a preoperative composite DeMeester score > 14.7 were considered eligible for the study. Eligible patients were interviewed regarding symptomatology and use of anti-secretory medication. Consenting patients underwent esophagogastroscopy (EG) with Congo red staining and biopsy of labeled regions. They also had repeat pH monitoring and esophageal motility studies (EMS). Results: Of the 19 patients who consented to the study, 17 were females. The average age was 46.8 years (range 28-57). The average decrease in BMI was 18.6 (range 7-34). Eight patients (42%) were symptomatic and remained on anti-secretory medication. The average interval from surgery to EG and pH testing was 13 months (range 3-36). The average preoperative DeMeester score was 48.4 and postoperative score was 31.6 (p = 0.3). DeMeester scores normalized in 41% of patients. Gastric pouch mucosa was Congo red positive in 84% of patients, and biopsies confirmed the presence of parietal cells in 89% of patients. Gastric pouch length did not influence GERD symptoms, pH scores, or presence of parietal cells. There was also no correlation between postoperative symptoms and postoperative DeMeester scores. Conclusions: Objective tests demonstrate persistent acid production and acid reflux in the majority of patients tested. RYGB, however, eliminated GERD symptoms in over half of morbidly obese patients. The mechanism for this effect is unclear and is probably unrelated to exclusion of acid-producing gastric mucosa.