Dietary supplementation of glutamine prevents intestinal dysfunction and atrophy in weanling piglets, but the underlying mechanism(s) are largely unknown. This study was conducted to test the hypothesis that weaning or glutamine may modulate expression of genes that are crucial for intestinal metabolism and function. In Expt. 1, we obtained small intestine from 28-d-old pigs weaned at 21 d of age and from age-matched suckling piglets. In Expt. 2, piglets were weaned at 21 d of age and then had free access to diets supplemented with 1% L-glutamine (wt:wt) or isonitrogenous L-alanine (control). At d 28, we collected small intestine for biochemical and morphological measurements and microarray analysis of gene expression using the Operon Porcine Genome Oligo set. Early weaning resulted in increased (52-346%) expression of genes related to oxidative stress and immune activation but decreased (35-77%) expression of genes related to macronutrient metabolism and cell proliferation in the gut. Dietary glutamine supplementation increased intestinal expression (120-124%) of genes that are necessary for cell growth and removal of oxidants, while reducing (34-75%) expression of genes that promote oxidative stress and immune activation. Functionally, the glutamine treatment enhanced intestinal oxidative-defense capacity (indicated by a 29% increase in glutathione concentration), prevented jejunal atrophy, and promoted small intestine growth (+12%) and body weight gain (+19%) in weaned piglets. These findings reveal coordinate alterations of gene expression in response to weaning and aid in providing molecular mechanisms for the beneficial effect of dietary glutamine supplementation to improve nutrition status in young mammals.