Abstract Background: Periodontal pathology in children has distinctive characteristics that can be accounted for by the peculiarities of the age, the dynamically changing oral environment, and the processes of formation and stabilization of periodontal structures during teeth eruption. Aim: The aim of this study was to investigate the composition of the subgingival microbiota during permanent dentition formation in puberty. Materials and methods: The study included 30 children aged between 10 and 15 years without gingivitis (up to 25% PBI), with good oral hygiene, with no systemic diseases or reception of antibiotics for 3 months. The clinical status of all children was assessed using a specially designed chart based on the periodontal examination chart of a child adopted by the Department of Pediatric Dentistry, FDM-Sofia. Gingival sulcus samples were taken with a paper pin from 6 teeth for a PCR – Real Time study of 9 control strains (a comprehensive sample). The samples were sent for investigation in standardized containers. Results: C. gingivalis (green complex) was found in almost all tested children and F. nucleatum (orange complex) - in more than half of them. The rest of the tested samples for microorganisms was isolated in just few of the children (6% - 17%). A. actinomycetemcomitans and P. gingivalis were not isolated in this study. Conclusion: The results of the study suggest that a significant amount of the periodontal pathogens migrate to the subgingival zone relatively early, immediately after the permanent teeth eruption, and become a risk factor for the development of periodontal disease.