One of the promising courses in the clinical dentistry is the use of molecular biological markers in patients with periodontal disease. First of all, this is due to the rising trend in the prevalence and risk factors of the disease, which makes relevant finding effective methods for early detection and preventive treatment. 30 patients diagnosed with generalized periodontitis of the I and II degree of severity were selected for the research. In the experimental groups of patients, an immunoassay was used to determine the marker level of bone marrow metabolism (MMP-8) in the oral fluid, in the dynamics of treatment. During the study, the content of this enzyme was found to be indicative of the transformation of the inflammatory process in the gums into the destruction of the alveolar bone.