The goal of this study was to evaluate the preventive effect of free glutamine versus N-acetyl-L-glutamine, a liquid-stable source of glutamine, on gut damage induced by protein energy malnutrition in pigs. Healthy pigs (n = 6) were fed a liquid formula for 30 days. Three subgroups of malnourished pigs (n = 6) received daily 20% of the food intake recorded in control group, supplemented with calcium caseinate, glutamine, or N-acetyl-L-glutamine. Body weight was recorded, and small intestinal samples were evaluated for biochemical and immunologic parameters. Suppression in body weight gain was significantly lower in pigs fed with N-acetyl-L-glutamine than in the rest of malnourished pigs. Total number of lymphocytes, CD21+ B cells and CD4+ T cells in ileal Peyer patches were not significantly different in malnourished pigs fed with N-acetyl-L-glutamine and in healthy pigs. In conclusion, N-acetyl-L-glutamine has a moderate protective effect, partially preventing changes induced by protein energy malnutrition.