Intestinal, nasopharyngeal microbiocenoses in children aged from 1 month till 6 years living in the various Irkutsk region cities were studied. The characteristic of the atmospheric air pollution level and estimation of the assumed risk for population health in these cities was given. Comparative analysis results of the quantitative and qualitative microflora structure in children biocenoses in the cities with various technogenic loading were given. Regional features of microbiota in the studied biotopes were shown. For the first time studying of bifidobacteria microecological cenotipes in studied territory was carried out. Data on a bifidobacteria species rating under existing technogenic loading conditions were obtained. «Indicator» microorganisms in children from various cities were established. Low antagonistic activity of bifidobacteria regional strains against opportunistic microorganisms was revealed.