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This study evaluated the efficacy of photodynamic therapy using the photosensitizer azulene and low-intensity laser associated with standard root chemical-surgical preparation (performed with 0.5% sodium hypochlorite) in dogs. Twenty animals from the Veterinary Hospital of the School of Veterinary Medicine and Animal Science, University of São Paulo (HOVET-FMVZ/USP) and treated at the Compared Dentistry Laboratory (Laboratório de Odontologia Veterinária [LOC]-FMVZ/USP) were included. Each subject possessed one single rooted tooth with complete root formation, pulp necrosis, complicated crown fracture and periapical bone rarefaction at the time of the radiographic examination. The endodontic treatment was performed in all dogs, which were divided into two equal groups. For group one, the standard chemical-surgical preparation was followed by the photodynamic therapy to evaluate the role of azulene after instrumentation. For group two, the photodynamic therapy was followed by the standard chemical-surgical preparation to evaluate the antimicrobial action of azulene before instrumentation. The results show that intracanal photodynamic therapy is efficient in eliminating unspecified bacterial and Enterococcus organism loads. In addition, this therapeutic modality reduces yeast contamination. The photodynamic therapy showed similar efficacy compared to standard chemical-surgical preparation. The application order of therapeutic modalities does not influence intracanal disinfection in both cases. This study shows that photodynamic therapy with low-intensity laser and azulene as a photosensitizer is a feasible alternative for improving treatment outcomes in routine practice of veterinary dentistry.