The aim of the study was to study the microflora of periodontal pockets and gingival fluid; determine the qualitative composition of periodontal pathogens by PCR; to determine the main associations of microorganisms, to determine the periodontal index in patients with cement caries, external pathological resorption and in patients from the comparison group. The examination included 80 patients, including 28 patients with a diagnosis of cement caries, 25 patients with a diagnosis of external cervical root resorption, 27 patients in the comparison group without tooth root damage. Based on the results of microbiological studies in various clinical conditions of the oral cavity, in particular, in different forms of lesions of the periodontium and hard tissues of teeth, the predominant microbial representatives and their combinations were identified. According to the study, it was revealed that all patients with cement caries and external pathological resorption have pathological processes arising in the periodontium. The study of the qualitative composition of the microflora showed that in patients with cement caries, the following associations of microorganisms are most often found: Aggregatibacter actinomycetemcomitans, Prevotella intermedia, Tannerella forsythia, Porphyromonas gingivalis, Candida albicans, Treponema denticola. Patients with external pathological resorption of microorganisms were found in patients with external pathological resorption of microorganisms: Prevotella intermedia, Treponema denticola, Candida albicans, Tannerella forsythia, Porphyromonas gingivalis, Epstein-Barr virus. These periodontal pathogenic microorganisms have a wide range of pathogenicity factors, which allows them to induce a prolonged inflammatory process. The study of the microflora of periodontal pockets and gingival sulcus in case of caries of cement and external pathological resorption is an important link in preventing the development and aggravation of pathological conditions of hard tissues of the tooth root and periodontal tissues.