The role of bacterial microflora of the human digestive tract in supporting the protection of the organism against food-borne pathogens and antigens is described. The effect of bacterial microflora on the immune system of the mucous surface of the intestinal tract (GALT) and its effect on secretory function of the immune system, particularly regarding antibody, mainly IgA, secretion, are discussed. The modulating effect of commensals and probiotics on the innate immunity response and their direct influence on the specific response are dealt with as are digestive tract dysfunctions connected with changes in microflora and their prophylaxis. Attention is paid to the beneficial effect of probiotics on human health by indicating noninvasive ways of increasing natural immunity by these microorganisms. There is a necessity to understand the mechanisms of the induction of the immune response by probiotic bacteria responsible for maintaining the organism in an alert state in the defense against pathogens.