Purpose: Breath hydrogen (H2) and methane (CH4) concentrations were used as a marker of colonic fermentation by gut flora in previous studies. Bacteria represent the sole source of gut H2, making this particular gas attractive for the identification of bacterial overgrowth states. The required concentration of these bacteria, under normal circumstances, seemes to be only found in the colon. However, in patients who had hydrogenic or methanogenic bacteria in the stomach, H2 or CH4 gases should be produced and consumed by their bacteria following ingestion of carbohydrates. Therefore, we attempted to measure the intragastric H2 and CH4 concentrations to determine the bacterial overgrowth in the stomach. Methods: Studies were performed in 700 consecutive patients undergoing esophagogastroscopy. At the time of endoscopic examination, we intubated the stomach without inflation by air, and 20 ml of intraluminal gas samples of both sites was collected through the biopsy channel. Intraluminal hydrogen concentrations were measured by gaschromatography. Results: The mean values of intragastric H2 and CH4 gas were 10.5 +/- 15.9 (0–219) and 3.2 +/- 4.9 ppm (0–53), respectively. Intragastric H2 differed more widely among subjects than intragastric CH4. If the intragstric H2 or CH4 levels more than 10 ppm was considered as the positive result of bacterial overgrowth in the stomach, 185 (26%) patients was positive. The intragastric hydrogen level was the highest in gastritis group followed by duodenal ulcer group and gastric ulcer group. The intragastric H2 level was significantly higher in patients without atrophic gastritis than in those with atrophic gastritis. There was no difference in intragastric CH4 concentrations between patients with and without atrophic gastritis. Conclusions: Unexpectedly, intragastric H2 or CH4 concentrations more than 10 ppm was detected in 26% of all subjects in this study. Although it is unknown whether intraluminal fermentation is related to digestive diseases, a large amount of intragastric H2 and CH4 may cause abdominal symptoms. We have to make a further study to evaluate whether bacterial overgrowth in the stomach is associated with some clinical symptoms or gastrointestinal diseases.