BACKGROUND Intestinal ischemia-reperfusion (I/R) injury plays an important role in the pathogenesis of systemic inflammation and multiple-organ failure. We studied whether glutamine, the primary fuel of the small intestine, prevents intestinal mucosal damage after intestinal I/R in rats. METHODS Rats were randomly divided into 4 groups: a sham-standard amino acid (SAA) group (n = 8); a sham-glutamine (Gln) group (n = 8); an I/R-SAA group (n = 10); and an I/R-Gln group (n = 9). Alanyl-glutamine solution was produced by replacing 36% of the total amino acid nitrogen with Gln. The superior mesenteric artery was ligated. After 60 minutes of ischemia, reperfusion was initiated and infusion was started. After 24-hour reperfusion, the intestinal segment was removed for morphological and biochemical analysis, and blood samples were drawn from the portal vein. Fluorescein isothiocyanate-conjugated dextran 70,000 (FITC-dextran) was infused into the duodenum 2 hours before animal death. RESULTS In the I/R-SAA group, extensive epithelial sloughing and mucosal ulceration of villous tips were observed, whereas these findings did not occur in the I/R-Gln group. Mucosal wet weight, DNA, and protein content decreased significantly in the I/R-SAA group compared with the sham-SAA group and increased significantly in the I/R-Gln group compared with the I/R-SAA group. Plasma FITC-dextran significantly increased in the I/R-SAA group compared with the sham-SAA group, but the plasma level in the I/R-Gln group was comparable with that of each sham group. Mucosal glutaminase activity significantly increased in both the I/R-SAA and I/R-Gln groups compared with the sham-SAA and sham-Gln groups, respectively. CONCLUSIONS Alanyl-glutamine protects against morphologic and functional mucosal injury after intestinal I/R in rats.