Enteropathy defines abnormalities of the small intestinal mucosa of various etiologies in which nutrition has a causal or a therapeutic role. Breast milk is the gold-standard feeding during infancy for optimal nutrition in health and the majority of diseases. Therapeutic formulae have decreased the need for enteral or parenteral support. Gastrointestinal infections are worldwide the most frequent cause of enteropathy by increasing mucosal permeability, local expression of costimulatory molecules allowing antigen penetration in the mucosa, and T-cell activation leading sometimes to disruption of oral tolerance. Concomitant malnutrition impairs not only the immunologic response but also the recovery of damaged mucosa with secondary intestinal and pancreatic enzymatic reductions. Optimal nutritional rehabilitation is the cornerstone of the management of persisting diarrhea. Celiac disease and cow's milk protein allergy are examples of chronic enteropathy. Multiple food allergies, even during breast-feeding, are increasingly reported due to an impaired development of oral tolerance. The dietary approach to allergic disease is currently evolving from passive allergen avoidance to active modulation of the immune system to (re)establish tolerance. The gastrointestinal flora provides maturational signals for the lymphoid tissue, improves balance of inflammatory cytokines, reduces bacterial invasiveness and dietary antigen load, and normalizes gut permeability. The clinical effects of nucleotides and zinc merit further clinical evaluation. Major attention has recently focused on the immune effects of dietary lipids in terms of possible prevention of allergic sensitization by downregulating inflammatory response and protecting the epithelial barrier and host-microbe interactions modifying the adherence of microbes to the mucosa.