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Practitioners are not successful in implemented treatments due to the great difficulty in completely removing bacterial deposits and their endotoxins. This study aimed to evaluate the capacity of photodynamic therapy to reduce the numbers of viable bacteria in periodontal pockets. Microbiological samples were collected before and after scaling and after photodynamic therapy. Photodynamic therapy was performed through the insertion of the photosensitizer toluidine blue and Endo PTC into the pocket for 3 min, followed by photosensitization with low-intensity diode of 4 J/cm². The results (log₁₀) were submitted to a descriptive analysis and a t-test. A reduction of 81.24% in the numbers of bacteria after scaling was observed, as well as 95.90% after photodynamic therapy (P < 0.01). Photodynamic therapy is indicated as an adjuvant treatment to reduce the numbers of viable bacteria in periodontal diseases.