The intestinal mucosal surface is colonised by the comensal microflora that attains very high numbers of bacterial cells in the distal intestine, more specifically in the colon. At the same time these extensive areas are the interface with the external environment, through which most pathogens initiate infectious processes in mammals. Intestinal mechanisms of defense need to discriminate accurately between comensal, symbiotic microflora, and exogenous pathogens. Today we do not fully understand the essence of the mechanism of discrimination but, probably, innate as well as adaptive immune responses participate in this process. We have explored, in in vitro models, the capacity of mucosal immunocompetent cells to discriminate amongst signals delivered by different types of bacteria. We have found at least two different patterns of innate response to gram-negative and gram-positive bacteria, and within this last group big differences are observed between species. We have only worked with non-pathogenic bacteria in what may represent the modulation of the physiological host status. The understanding of these modulatory functions could render a unique possibility for the use of food-borne bacteria to prevent or correct intestinal problems associated with food allergy, inflammatory bowel disease, and autoimmunity.