Polymerase chain reaction (PCR) shows a high specificity and allows us to identify pathogenic periodontal bacteria. We chose 45 patients wich were divided into three groups with various types of treatment: (I) - SRP; (II) - SRP, followed by topical application of antiseptics (SRP + local); (III) - SRP followed by systemic administration of antimicrobial agents (SRP + systemic). We collected samples from the initial time (TO) and one month after the treatment (T1) for each patient. For the microbiological assessment of periodontal therapy, we analyzed 90 subgingival plaque samples using PCR technique which provides qualitative data on five periodontopathogenic bacteria species: A. actinomycetemcomitans, P.gingivalis, P.intermedia, T.forsythia, and T.denticola. The treatment was followed by a qualitative change of the bacteria detected previously in a different ratio depending on the treatment. We found the inefficiency of mechanical treatment regarding the reduction of periodontal bacteria in patients belonging to group I, an improvement in the results of group II, while the treatment in group III proved to be the most effective . In patients detected A.a+ and/ or P.g+ a systemic antibiotic treatment is required because these periodontal bacteria penetrate the tissue and mucosal surfaces of the oral cavity.