The gastrointestinal tract communicates directly with the external environment. Necessary nutrients must be absorbed and commensal bacteria tolerated, and foreign proteins, antigens, and pathogens must be simultaneously excluded or destroyed. Immaturity or disruption of the mucosal immune defenses increases vulnerability to food allergy, intolerance, and infectious disease. Diseases resulting from ingested foreign proteins and organisms are increasing and cause morbidity and mortality worldwide. There is no specific treatment for food allergy other than avoidance. Vaccination for infectious disease is limited by the cost and logistics of distribution and administration, particularly in developing countries. Novel strategies are being explored to modulate the gut mucosal immune system by altering protein expression in food. Crops are being developed to remove deleterious allergens to prevent immunogenic exposure while preserving nutritional quality. Local food plants that express protein fragments of pathogens might provide an effective means to stimulate gut mucosal immunity while increasing vaccine accessibility.