Progressive peri-implant bone losses, which are accompanied by inflammatory lesions in the soft tissues, are referred to as peri-implantitis. The aim of this study was to compare the effects of photodynamic therapy (PDT) and conventional technique on microbial reduction in ligature-induced peri-implantitis in dogs. Eighteen third premolars from nine Labrador retriever dogs were extracted and the implants were submerged. After osseointegration, peri-implantitis was induced. After 4 months, ligature was removed and natural bacterial plaque was allowed to form for another 4 months. The animals were then randomly divided into two groups. In the conventional group, they were treated using mucoperiosteal flaps for scaling the implant surface and chlorexidine (conventional) irrigation. In the PDT group, only mucoperiosteal scaling was carried out before photodynamic therapy. Inside the peri-implant pocket, a paste-based azulene photosensitizer was placed and then a GaAlAs low-power laser (lambda=660 nm, P=40 mW, E=7.2 J for 3 minutes) was used. Microbiological samples were obtained before and immediately after treatment. Before treatment, one implant was removed and analyzed by scanning electron microscopy to validate the contamination. The results of this study showed that Prevotella sp., Fusobacterium sp., and S. Beta-haemolyticus were significantly reduced for both groups. After treatment, no significant differences were observed between the groups. These findings suggest that photodynamic therapy is a non-invasive method that could be used to reduce microorganisms in peri-implantitis. J Periodontol 2005;76:1275-1281.