The examination of nasopharyngeal and intestinal microbiocenoses was implemented in orphan children aged 1-3 years residing in children;s home of Cheremkhovo of the Irkutskaia oblast. All children had compromised anamnesis: prematurity, hypotrophy, chicken pox, frequent acute respiratory viral infections, intestinal infections, atopic dermatitis. The study was carried out to comprehensively evaluate conditions of intestinal and nasopharyngeal biotops in children residing in closed children’s institution - children’s home. The microbiological analysis of qualitative and quantitative composition of content of intestine and nasopharynx was implemented according standard techniques. The analysis established in 81.2±6.90% of examined children deficiency of Bifidobacterium flora, decreasing of level of population density of bifidobacteria up to 6.9±1.53% lg KOE/g, in 31.2±8.1% - deficiency of normal colibacillus, in 78.1±7.3% - increased level of opportunistic flora. The analysis also established high rate of isolation of Escherichia coli with decreased enzyme activity and in 28.1±7.9% - Escherichia coli with hemolytic activity. The enterococci were permanent participants of nasopharyngeal and intestinal biotop (58.6±8.7%). From opportunistic flora, in nasopharynx were registered pathogenic streptococci - S.pyogenes, S.pneumonia and also pathogenic fungi Candida andpoly-resistant strains S. aureus. The study results demonstrated characteristics of microbial ecology of intestinal and nasopharyngeal biotops of orphan children in conditions of children institution of closed type where the circulation of pathogenic and opportunistic microorganisms occurs intensively, including strains with high medicinal resistance. All this determines necessity to attribute alumni of children’s homes to risk group of infectious pathology and requires constant micro-ecological monitoring for timely correction of microbiocenoses.