Enteropathy defines abnormalities of the small intestinal mucosa, visible with the light microscope, of various etiologies, that can be separated into acute versus chronic conditions. This review focuses on these areas in which recent progress has been made. Severe infections increase mucosal permeability and induce local expression of co-stimulatory molecules allowing antigen penetration in the mucosa, T cell activation and possible disruption of oral tolerance. Biotherapeutics are of importance in the prevention and treatment of (chronic) enteropathy of infectious origin. Celiac disease and cow's milk protein allergy are key examples of chronic enteropathy. The dietary approach to allergy has evolved to include active stimulation of the immature immune system in order to support the establishment of tolerance. Supplementation with probiotics may provide maturational signals for the lymphoid tissue and improve the balance of pro- and anti-inflammatory cytokines. Enteral polymeric feeding is effective in Crohn's disease. Dietary nucleotides may improve growth and immunity, optimize maturation, recovery and function of rapidly dividing tissue. Adequate dietary lipids are important not just for caloric value but also for immune-modulatory effects. Lipids may prevent allergic sensitization by downregulating inflammatory response (n-3 but not n-6 fatty acids) whilst protecting the epithelial barrier, regulating immune function and modifying the adherence of microbes to the mucosa, thereby contributing to host-microbe interactions.