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The results are presented of a comprehensive  study in 108 children aged 6 months up to 12 years, suffering various variants of mycoplasmal and herpesvirus infections (HVI): in mono and mixed combinations. The aim of the study was a comparative assessment of the state of the microbiota of the two main biotopes, the oropharynx and the intestine, depending on the variant of mycoplasmosis and HVI flow.A correlation  was established between the depth of dysbiosis of these biotopes, the variant of the course of mycoplasmosis and HVI, and cardiovascular disorders. Immunological criteria for the formation of post-inflammatory fibrosis of blood vessels and heart valves against the background of vasculitis in mycoplasmal-herpesvirus infection have been determined.