The intestines are an important organ responsible for nutrient absorption, metabolism and recognition of food signals. The organ also acts as a physical and biological barrier against harmful substances including food pathogens and environmental chemicals. Food-derived peptides with a variety of physiological functions have been discovered in the past several decades. Although dietary peptides would mostly be hydrolyzed by digestive enzymes in the intestinal tract, possibly losing their biological functions during this step, some could be absorbed intact and act in their target organs. The intestines are also one of the targets for functional peptides. The intestine-modulatory peptides can be classified into two categories: (1) peptides that express their functions in the intestinal tract and (2) peptides that modulate intestinal epithelial cell functions. The 1(st) group includes peptides that regulate the intestinal absorption of nutrients. Enhancing mineral absorption by casein phosphopeptides, and suppressing dietary cholesterol absorption by soybean peptides are typical examples. The 2(nd) group includes such glutamine-containing peptides as Ala-Gln that show interesting properties in preventing and/or repairing damage caused by oxidative stress and inflammatory reactions. We have found that carinosine (beta-Ala-His) suppressed the secretion of such inflammatory cytokines as IL-8 in human intestinal epithelial cells, suggesting its anti-inflammatory function in the intestines. Peptides that modulate such intestinal immune functions as secretory IgA production and cytokine secretion, and opioid peptides regulating intestinal motility are also included in this group. These intestine-modulatory peptides would be useful as ingredients of future functional foods to prevent lifestyle-related diseases and promote gut health.