Background. The article presents modern views on the role of microbiota in the occurrence of atopic pathology. The reasons for the decline in biodiversity, changes in the dynamic balance between macro-microorganisms, violation of the colonization of human ecological niches, which are important in the formation of local and systemic immunity, are considered; the main causes of dysbiosis at an early age, which precedes the formation of allergic diseases (food allergy, atopic dermatitis, allergic rhinitis, asthma), a significant increase in which has been noted in recent decades. Aim: to analyze reviews, articles devoted to the study of the role of the human microbiota, a decrease in its biodiversity in the formation of allergic pathology. Methods: the use of analytical reviews, articles posted in electronic databases: PubMed, Scopus, Web of Science, position of the European Academy of Allerogology and Clinical Immunology (EAACI). Conclusion: the analysis made it possible to present the modern role of microorganisms inhabiting the ecological niches of the human body, their dynamic balance on the function of all organs and systems, with consideration of the reasons for the decrease in biodiversity and the subsequent development of allergic diseases; the need to further study the role of not individual pathogens, but the general properties of the microbial population, which will help to change the approach to disease therapy, based not on replacing individual microorganisms, but on restoring the all population.