Chronic apical periodontitis is an inflammatory disease of the tissues surrounding the tip of the tooth root, characterized by destruction of bone tissue and often asymptomatic. For a long time, the clinical diagnosis was made on the basis of X-ray and clinical studies. However, numerous studies by domestic and foreign authors have proved that the key link in the development and course of this disease is the microbial factor. The microbiological diagnostic method, which allows the identification of bacterial factors of the pathological process in the periapical tissues, opens the way to targeted and effective treatment. This article presents a microbiological analysis of the root canal system in chronic apical periodontitis. The overall results showed that the microbiome of the root canal system is a complex and highly organized ecosystem. A key characteristic of this ecosystem is its high taxonomic diversity, where the infectious process is supported not by a single pathogen, but by complex anaerobic polyassociations of microorganisms. This fact is of fundamental importance for understanding the pathogenesis of the disease and developing ongoing therapeutic strategies to increase the prognostic success of endodontic treatment and reduce the risk of recurrence of periodontal tissue pathologies.