Dental implants are now used broadly for recovering loss of masticatory function and esthetics. Although it has been revealed that dental implants can often survive long term, biological and mechanical complications may arise. Recent cross-sectional and retrospective studies noted a higher prevalence of peri-implantitis at the implant and subject level than previously considered. Additionally, once peri-implantitis occurred, it was more destructive and progressed rapidly compared with periodontitis because of different histological features (e.g., lack of healthy connective tissue seen around the teeth separating inflammatory cells from bone). Moreover, the predictability of peri-implantitis treatment is not as high as that of periodontitis treatment. The success of peri-implantitis treatment is associated with multiple factors, such as implant surface, disease severity, smoking habit, and surgeon’s experience. However conflicting results were observed in experimental studies focused on biocompatibility after cleansing contaminated titanium disks or implants. To date, a standard technique for cleansing contaminated surfaces affected by peri-implantitis has not yet been established clinically or even experimentally. Additionally, the titanium disk or other forms of titanium used in most in vitro studies to evaluate decontamination methods do not resemble the screw-shaped implants typically placed in clinical practice in terms of macro- and microstructures, rendering it difficult to extrapolate such results to the clinical setting. Moreover, a single bacterial species or artificial biofilms were often used to evaluate the efficacy of decontamination methods on the materials. The aim of this study is to evaluate the effect of several representative decontamination methods on biofilms formed intraorally on the implant surface using SEM for qualitative analysis and culture technique for quantitative analysis.