The alteration of the intestinal epithelial barrier is often a consequence of various intestinal diseases but may also be the starting point of these diseases. Undigested food antigens are transported across the intestinal epithelium by a transcytotic mechanism, including a processing within the enterocytes, and leading to the passage of intact proteins, peptides, and amino acids to the underlying mucosa. Inflammation and infection lead to the upregulation of the transport and processing of food proteins; for example, IFN gamma increases the rate of transcytosis and alters, like TNF alpha, the tight junction permeability. Infection of gastric digestive epithelia with Helicobacter pylori also increases the antigenic load transmitted to the underlying immune system by inhibiting the enterocytic lysosomal degradation of proteins. In allergic diseases, such as cow's milk allergy, TNF alpha may be involved in the intestinal dysfunction and the associated enteropathy.