Porphyromonas gingivalis (P. gingivalis) is considered to be major putative periodontal pathogens. The purpose of the study was to evaluate P. gingivalis and clinical effects of scaling and root planning (SRP) in 20 subjects after 3 months.Twenty periodontitis patients were selected. The mean age was (44.33 +/- 13.86) years old. Clinical assessments of probing depth (PD), clinical attachment loss (CAL) and bleeding on probing (BOP) were made prior to SRP and at 3 months post-therapy. Subgingival plaque samples were taken at each visit and analyzed using TaqMan real-time polymerase chain reaction for the presence and levels of P. gingivalis. The quantification for P. gingivalis was also performed with the help of the species-specific primers/probes and the serial dilution of the plasmid standards.Mean probing depth, mean clinical attachment loss and bleeding on probing showed significant reduction at 3 months (P<0.001). The prevalence and level of P. gingivalis were significantly reduced after SRP (P<0.001). A positive correlation was found between the numbers of P. gingivalis and PD at baseline (P<0.001). There were no correlation between the initial level of P. gingivalis at baseline and the clinical improvement after therapy. But the number of P. gingivalis at responding sites was more decreased than non-responding sites after SRP (P<0.05).SRP produced a good clinical improvement. The prevalence and level of P. gingivalis were significantly reduced after SRP. The effect of SRP may be determined by the degree of P. gingivalis is decreased. The real-time polymerase chain reaction can be used to evaluate the effect of periodontal therapy.