We have shown that phosphatidylcholine (PC) metabolites may have a function in counteracting the production of reactive oxygen species (ROS), and that this mechanism can lead to the generation of methane from choline. The aims were to establish whether the dietary administration of PC can protect the reperfused small bowel mucosa by its acting as an anti-inflammatory agent and to investigate this possibility in association with in vivo methane generation. Group 1 (n = 5) of anesthetized dogs served as sham-operated controls, whereas in groups 2 (n = 6) and 3 (n = 6), complete small intestinal ischemia was induced by occluding the superior mesenteric artery for 60 min. Groups 1 and 2 were fed with normal laboratory chow for 1 week before the experiments, whereas the animals in group 3 received a special diet containing 1% soybean PC. The intramucosal pH and the difference of the arterial and local PCO2 (PCO2 gap) were detected by indirect tonometry. Intestinal superoxide production and myeloperoxidase (MPO) activity (a marker of tissue leukocyte infiltration) were ascertained on ileal biopsy samples 180 min after reperfusion. The content of methane in the exhaled air was determined by gas chromatography. I/R was characterized by significant tissue acidosis with ROS generation and elevated MPO activity. These changes were accompanied by increased methane production in the exhaled air during reoxygenation. The PC-enriched diet prevented the decrease in intramucosal pH, diminished the intestinal superoxide generation and the MPO activity, and significantly decreased the exhaled methane concentration. The increased dietary uptake of PC exerts an anti-inflammatory influence in the gastrointestinal tract. Exhaled methane is linked to abnormal ROS generation; a decreased methane production is associated with significantly reduced inflammatory activation during I/R.