This study analyzed the antimicrobial effect of photodynamic therapy (PDT) in association with endodontic treatment. Twenty patients were selected. Microbiological samples were taken after accessing the canal, endodontic therapy, and PDT. At the end of the first session, the root canal was filled with Ca(OH)(2), and after 1 week, a second session of the therapies was performed. Endodontic therapy gave a mean reduction of 1.08 log. The combination with PDT significantly enhanced the reduction (1.83 log, p = 0.00002). The second endodontic session gave a similar diminution to the first (1.14 log), and the second PDT was significantly more effective than the first (p = 0.002). The second total reduction was significantly higher than the second endodontic therapy (p = 0.0000005). The total first + second reduction (3.19 log) was significantly different from the first combination (p = 0.00006). Results suggest that the use of PDT added to endodontic treatment leads to an enhanced decrease of bacterial load and may be an appropriate approach for the treatment of oral infections.