The article presents an analytical review of the works of domestic and foreign authors on the problem of studying the peculiarities of the formation of the intestinal microbiota and risk factors for the development of microdysbiosis in newborns with the activation of opportunistic bacteria, including C. difficile. Special attention is paid to the effect of antibiotics on the state of the intestinal microbiota and the activation of toxigenic strains of C. difficile. Divergent views on the role of toxigenic strains of C. difficile in the development of infectious pathology of newborns are presented.