Acute, inflammatory processes contribute to the fact that conventionally pathogenic and pathogenic microorganisms colonize the mucous membranes of the small intestine and form biofilms, can become a source of bacterial toxin, which, when the epithelial layer breaks, penetrates to the lymphatic and blood systems, contributing to the formation of sepsis. The barrier function of the epithelium is critical in the development of inflammatory bowel diseases, while normal functioning requires a constant balance between reactivity and tolerance to microorganisms of the intestinal lumen. Increased permeability of the intestinal mucosa is the main risk factor for the spread of bacteria. Epithelium, being an essential element of tissue barriers, provides selective transport for the movement of ions and macromolecules, and also creates an obstacle for their penetration into the underlying tissues. Control of the permeability of the epithelial layer is carried out by the apical intercellular complex - tight contacts, which comprise proteins of the claudine family. Intestinal flora affects the sensory, motor and immune functions of the intestine, and also interacts with higher nervous centers. Immunosuppressive processes are one of the main causes of destabilization of the barrier function, intestine, and brain.