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Data accumulated to date, including published data obtained by other researchers, were used to demonstrate that the immune system differentiates between the normal resident microflora of the body and transient microflora using pattern recognition receptors (PRRs) on the surface of cells. The body forms a regional tolerance to the former microflora, and the latter one is inhibited by the immune system and, upon entering the body, eliminated. This function of PRRs in lower organisms is exercised by the innate immunity; in higher organisms, the adaptive immunity is also involved. It is important that, in humans and other mammals, this function of control also extends to the central tolerance to clone elimination, determining the absence of an immune response to the body's own tissues.