The present study aimed to evaluate the acute locally injurious property of our most current hydroxyl radical generation system by hydrogen peroxide (H2O2) photolysis. This system, which releases 3% H2O2 with a 405-nm laser, was developed in our laboratory for the treatment of dental and periodontal infectious diseases. First, the hydroxyl radical yield generated by H2O2 photolysis was examined by applying an electron spin resonance-spin trapping technique. Second, the bactericidal effect of the device was examined under a simulant condition in which Streptococcus mutans, a pathogenic bacterial species that causes caries, was irrigated with running 3% H2O2 concomitantly with laser irradiation. Finally, the acute topical effect of the model apparatus on rat palatal mucosa was evaluated by histological examination. We found that the hydroxyl radical yield was dependent upon laser output power. The bacterial count was substantially reduced within as little as 3 min. No abnormal findings were observed in the palatal mucosa, even when rats received three treatments of 3% H2O2 with laser irradiation at an output power of 40 mW. These results suggest that our apparatus has the ability to kill bacteria via hydroxyl radical generation and is safe to use at the lesion site of dental and periodontal infectious diseases.