BACKGROUND The normal stomach is virtually sterile but the effect of Roux-en-Y gastric bypass (RYGBP) on bacterial flora in the used (very small proximal pouch) and unused (large bypassed) gastric chambers is not known. In a prospective study, this variable was documented. METHODS Bariatric subjects (n=37) were submitted to endoscopic examination of both gastric reservoirs via FUJINON enteroscope model EN-450P5, 7.3 +/- 1.4 years after RYGBP. Age was 42.4 +/- 9.9 years (70.2% females), preoperative BMI was 53.5 +/- 10.6, and current BMI was 32.6 +/- 7.8 kg/m2. Methods included quantitative culture of gastric secretion along with gastric pH and lactulose/hydrogen breath test. RESULTS None of the subjects displayed diarrhea, malabsorption or other complaints suggestive of GI bacterial overgrowth. Elevated counts of bacteria and fungi were identified in both chambers, with predominance of aerobes and anaerobes, but not molds and yeasts, in the proximal stomach. Gram-positive cocci, bacilli and coccobacilli represented the majority of the isolates. Gastric pH was neutral (pH 7.0 +/- 0.2) in the proximal pouch, whereas the distal chamber mostly but not always conserved the expected acidity (pH 3.3 +/- 2.2, P<0.001). The breath test for bacterial overgrowth was positive in 40.5% of the population. CONCLUSIONS 1) Frequent colonization of both gastric chambers was detected; 2) Aerobes, anaerobes and fungi were represented in both situations; 3) Gastric pH as well as bacterial count was higher in the functioning proximal stomach; 4) Breath test was positive in 40.5% of the subjects; 5) Clinical manifestation such as diarrhea, malabsorption or pneumonia were not demonstrated; 6) Further histologic and microbiologic studies of both the stomach and the small bowel are recommended.