Currently, there are no criteria allowing to adequately assess composition and volume of the newborns' gut microbiota, which prevents early detection of the pathological processes and appropriate intervention. This study aimed to apply the methods of culturomics, proteomics and molecular genetic technologies to investigate the development of gut microbiota in healthy newborns delivered in the city of Moscow both vaginally and through a cesarean section. We examined 66 children, 33 of them delivered vaginally and 33 by cesarean section. The luminal bacterial flora samples were collected on the 1st, 7th and 30th days of life. There were 136 species of microorganisms belonging to 40 genera identified. We established that cesarean section slows down normal development of the gut microflora: through the follow-up period (1 month of life), gut microbiocenosis in such children did not yield the results on par with those registered in children born vaginally. Bifidobacteria were significantly more common in the vaginal delivery group: 84% of 10⁹–10¹² CFU/g versus 33% of 10⁵–10¹² CFU/g in the cesarean section group. At the same time, the former group had significantly less clostridia (33.3% and 65.4%, respectively) and lactose-negative Escherichia coli strains (2.4 and 19.4%, respectively) than the latter group.