The use of NSAIDs (non-steroidal anti-inflammatory drugs), although of great therapeutic value clinically, is limited by their tendency to cause mucosal damage in the gastrointestinal tract. In the small intestine, the effects these drugs have been shown to produce include inhibition of cyclo-oxygenase, mitochondrial dysfunction and free radical-induced oxidative changes, all of which contribute to the mucosal damage seen. Glutamine is a fuel preferentially used by enterocytes and is known to contribute to maintaining the integrity of these cells. In the present study, we investigated the effect of glutamine on indomethacin-induced changes in the small intestinal mucosa. Rats were given 2% glutamine or glutamic acid or isonitrogenous amino acids, glycine or alanine, in the diet for 7 days. Indomethacin was then administered orally at a dose of 40 mg/kg of body weight. After 1 h, the small intestine was removed and used for the measurement of parameters of oxidative stress and mitochondrial and BBM (brush border membrane) function. Evidence of oxidative stress was found in the mucosa of the small intestine of drug-treated rats, as indicated by significantly increased activity of xanthine oxidase ( P <0.001) and myeloperoxidase ( P <0.001), with corresponding decreases in the levels of several free radical scavenging enzymes and α-tocopherol ( P <0.001 in all cases). Levels of products of peroxidation were also significantly elevated ( P <0.001 for all the parameters measured). In addition, oxidative stress was evident in isolated intestinal mitochondria and BBMs ( P <0.001 for all the parameters measured), with associated alterations in function of these organelles ( P <0.001 for all the parameters measured). Supplementation of the diet with glutamine or glutamic acid prior to treatment with indomethacin produced significant amelioration in all the effects produced by the drug in the small intestine ( P <0.001 for all the parameters measured). Glycine and alanine were found to be much less effective in these respects.