Purpose: The erbium: YAG (Er: YAG) laser is used for decontaminating implant surfaces in the treatment of peri-implantitis. In this study, we quantified lipopolysaccharides (LPS) before and after decontaminating the contaminated layer on the implant surface, using an Er: YAG laser. In addition, we report that the peri-implantitis of the patient improved, based on the results of clinical evaluation, bacteriological examination, and cone-beam computed tomography (CBCT). Patient: A 68-year-old woman visited our hospital with the chief complaint of drainage from an implant. Her implant superstructures had been installed eight years ago, and she had no systemic disease except periodontal disease. X-ray examination revealed high resorption of the alveolar bone around the implant, and CBCT images revealed bone resorption; the resorbed bones were half the length of the implant. In addition, bacterial examination of the peri-implant pocket revealed Tannerella forsythensis, Treponema denticola, and Fusobacterium nucleatum. Although the implant showed no mobility, the probing periodontal pocket depth (PPD) of the labial center was 14 mm, and the distopalatal PPD was 10 mm. After the initial periodontal therapy, the PPD was 10-13 mm, and it bled on probing. Therefore, a surgical procedure was performed to treat the peri-implantitis. After administration of anesthesia, a full-thickness flap was raised, and a vertical bone defect with three walls on the apical side and one wall on the crown side was observed. The inflammatory tissue around the bone defect and the implant surface were decontaminated using an Er: YAG laser with water spray. LPS on the implant surface were sampled twice before and after decontamination and quantified using the Limulus amebocyte lysate method. The average of all the values was used as the LPS value, which decreased from 10.3755 to 0.0015 EU/ml. Bio-Gide was applied after insertion of Bio-Oss, and the flap was repositioned and sutured. Results: The PPD of the implant site stabilized at 2-3 mm 10 months after the procedure. A comparison of periodontal disease-related bacterial tests before and 12 months after surgery revealed that the numbers of T. forsythensis, T. denticola, and F. nucleatum decreased after surgery. Newly formed bone was observed in the intrabony defect from the CBCT images. Conclusion: In this case, the contaminated layer on the implant surface was decontaminated by an Er: YAG laser used for the treatment of peri-implantitis, along with reduction of LPS on the implant surface, facilitating long-term bone regeneration.