The efficacy of air-polishing on subgingival debridement, as compared to scaling and root planning (SRP), was evaluated clinically and microbiologically. Fifteen patients diagnosed as chronic periodontitis, and having single-root tooth over 5 mm of pocket depth symmetrically in the left and right quadrant, were investigated. Subgingival debridement was performed by SRP and air-polishing. The results were evaluated and compared clinically and microbiologically. Probing pocket depth (PPD), bleeding on probing (BOP), relative attachment level (RAL) and change of gingival crevicular fluid (GCF) were assessed before treatment, and at 14 and 60 days after treatment. Microbial analysis was done pre-treatment, post-treatment, and at 14 and 60 days after treatment. Results of air polishing showed that post treatment, the PPD and BOP decreased, and attachment gain was observed. There was no clinical difference when compared to SRP. The volume of GCF decreased at 14 days, and increased again at 60 days. Compared to SRP, there was a statistical significance of the volume of GCF at 60 days in air-polishing. In the microbial analysis, high-risk bacteria that cause periodontal disease were remarkably reduced. They decreased immediately after treatment, but increased again with the passage of time. Thus, our results show that subgingival debridement by air-polishing was effective for decrease of pocket depth, attachment gain, decrease of GCF and inhibition of pathogens. Further studies are required to compare air-polishing and SRP, considering factors such as degree of pocket depth and calculus existence.