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Aim. This work was undertaken to assess the effect of 120-day isolation conditions in a sealed compartment with an artificial habitat on the formation of microbiocenosis and the system of signaling image-recognizing receptors of the Toll-like (TLR) family of innate immunity.Materials and methods. The microflora of the intestine and upper respiratory tract, as well as the content of monocytes and granulocytes expressing TLRs (TLR1, TLR2, TLR4, TLR6, TLR9) in the peripheral blood, and the basal production of cytokines (IL-1β, IL-6, IL-8, IL-10, TNF-α) by immunocompetent cells of six volunteers was studied. To prevent intestinal and upper respiratory tract dysbiosis, two groups of medication were used: commercial strains (Linex and Bifidumbacterin Forte) and autoprobiotics made on the basis of protective microflora representatives isolated from each individual before the experiment.Results. The studies showed that the stay of a healthy person in an artificial environment had a significant impact on the state of microflora and the system of TLRs of innate immunity cells. This work demonstrates for the first time unidirectional changes in the absolute content of monocytes in the peripheral blood expressing TLR1, TLR2, TLR4, TLR6, TLR9, and the total microbial count in the gastrointestinal tract and in the upper respiratory tract from the 30th to the 120th day of the experimental exposure. Oral administration of autoprobiotic medication contributed to a decrease in the content of opportunistic microflora, while maintaining a high level of protective intestinal microflora, as well as an increase in the production of TNF-α and IL-10 by immunocompetent peripheral blood cells in vitro.