Among microorganisms found in the oral cavity there are several kinds of periodontopathogenic bacteria having higher adhesive, invasive and toxic properties. Eighty patients with moderate and severe chronic generalized periodontitis were included in the study. The choice of treatment regimen depended on real-time PCR values of pathogenic microorganisms in periodontal pockets. Data on composition of periodontal pockets microflora by moderate and severe periodontal disease allow prompt target antimicrobial therapy.