This review discusses pathogenetic aspects of interaction between microbiota of the gastrointestinal tract and the hepatobiliary system. The results of works indicating the role of violations of microbiocenosis of the small intestine (bacterial overgrowth syndrome) and the colon in the development of diseases of the liver and biliary tract are presented. Further studies are needed to clarify the impact of altered intestinal microflora on the state of the hepatobiliary system that would help to optimize approaches to the treatment of these patients, in particular, a combination of probiotics and preparations of bile acids.