Background Initial periodontal therapy (IPT) is cornerstone of periodontal therapy and the first step to control of periodontal risk factors. Scaling and root planing are used to treat root surface irregularities and remove virulent factors caused by periodontal pathogens. This procedure also incorporated into periodontal surgery. To elucidate the effects of IPT on prevalence of Epstein-Barr virus (EBV) DNA and Porphyromonas gingivalis , we used subgingival plaque samples from chronic periodontitis (CP) patients.Methods Seventeen CP patients were recruited and determined measured periodontal status clinical parameters such as by probing depth (PD), clinical attachment level (CAL), bleeding on probing (BOP) and an X-ray examination, and subgingival plaque samples were collected from two periodontal sites with PD of < 3 mm (healthy sites: HS) or > 5 mm (periodontitis sites: PS) at first visit and after IPT. Plaque samples were subjected to a real-time PCR to detect EBV DNA and P. gingivalis.Results EBV DNA and P. gingivalis were detected 9 (52.9%) and 14 (82.3%) sites within the subgingival samples from HS, and 13 (76.5%) and 14 (82.3%) sites within the PS at first visit. After IPT, number of detections of EBV DNA and P. gingivalis were decreased to 5 (29.4%) and 13 (76.5%) sites within the subgingival samples from HS, and 9 (52.9%) and 10 (58.8%) sites within the PS. Significant improvements in PD and BOP were observed after IPT in PS. Coexistence of EBV DNA and P. gingivalis in the subgingival samples from PS at first visit (12 sites; 70.6%) were significantly decreased after IPT (6 sites; 35.3%).Conclusion These results suggest that the IPT was effective in improvement of clinical parameters such as PD and BOP and reducing the coexistence of EBV and P. gingivalis in the subgingival plaque from PS. However, IPT could not eradicate the EBV and P. gingivalis . Further research would be necessary for improving the periodontal treatment strategy.