In this study, the effects of pulsed Nd:YAG laser irradiation on the apical seat and periapical region of instrumented root canals were investigated. One hundred and ninety-two teeth, including incisors and molars (239 root canals), in 18 healthy adult beagle dogs were used. After extirpation of the pulp under anaesthesia, each root canal was shaped up to at least a size 40 K-file, and then laser irradiated using the following parameters: 1 W, 15 pps for 2, 3, and 4 s; 2 W, 15 pps for 2 s. The effectiveness of debris removal and carbonization on the root canal walls immediately laser irradiation were examined and inflammation of the periapical region at 1, 2, and 4 weeks after laser irradiation was examined using light microscopy. Effective debris removal was observed in most cases in the laser-treated groups and was dependent on irradiated energy. Carbonization was observed in the irradiated root canals except at the parameter of 1 W for 2 s. Periapical inflammation was observed at 1 W for 2 s to the same extent as in the control group (P > 0.01). These results suggest that the pulsed Nd:YAG laser is useful for debris removal with no adverse effects immediately after extirpation of the pulp if appropriate parameters are selected.