Background: Porphyromonas gingivalis, Bacteroides forsythus, and Actinobacillus actinomycetemcomitans have been described as periodontopathic bacteria, and their presence in subgingival pockets can lead to development of periodontal disease. Until now, clinical parameters have been used to evaluate the effect of conventional periodontal treatment without microbiological parameters. The present study examined the microbiological effects of initial periodontal therapy using DNA probes and the polymerase chain reaction (PCR)., Methods: Twenty-six patients with periodontitis, 10 males and 16 females, were given instructions regarding oral hygiene, then thoroughly treated by conventional scaling and root planing. Bacterial samples were collected on paper points from 4 sites per patient at baseline and after initial therapy (total: 104 sites). Clinical parameters including probing depth, attachment level, and bleeding on probing were also recorded for each site at baseline and after therapy. A DNA probe kit was used to monitor the frequency of B. forsythus, P. gingivalis, and A. actinomycetemcomitans, the last of which was identified by PCR., Results: At baseline, B. forsythus was the bacterium most frequently detected. DNA probe analysis also showed that more than half of the sites were colonized by both B. forsythus and P. gingivalis. Initial therapy resulted in significant clinical improvement such as significant reduction in the frequency of B. forsythus and P. gingivalis detected using the DNA probe. A. actinomycetemcomitans was difficult to detect using the DNA probe, but PCR indicated that levels of A. actinomycetemcomitans did not significantly decrease., Conclusions: These results indicate that initial conventional therapy can eliminate B. forsythus and P. gingivalis, but not A. actinomycetemcomitans. When levels of these bacteria decreased to below-detectable levels, clinical improvement was significant. These results indicate that monitoring levels of these three periodontopathic bacteria may render periodontal therapy more effective and accurate.