High-power pulsed lasers have been recently regarded to be anabolic to bone, but in vivo evidence is still lacking. This study aimed to investigate the capacity of bone repair using a high-power, Q-switched, pulsed, neodymium-doped yttrium aluminium garnet (Nd:YAG) laser, using bilateral calvarial defect models having non-critical sized, 5 mm (rat) or 8 mm (rabbit) diameter. One of the bilateral defects, which were all filled with collagen sponge or left empty, was irradiated with a Nd:YAG laser once every 2 days for 2 weeks at a constant total fluence rate (344 J/cm(2) ), output power (0.75 W), pulse repetition rate (15 pps) and wavelength (1064 nm) and examined for the laser effect. The same experimental scheme was designed using a rabbit calvarial defect model implanted with sponge, which was explored for the dose effect of output power at 0.75 and 3 W with the same quantities of the other parameters. New bone formation was evaluated by micro-computed tomography-based analysis and histological observation at 4 weeks after surgery. Laser irradiation significantly increased new bone formation by approximately 45%, not only in the sponge-filled defects of rats but also when the defects were left empty, compared to the non-irradiated group. Consistently, both doses of output power (0.75 and 3 W) enhanced new bone formation, but there was no significant difference between the two doses. This study is one of the first to demonstrate the beneficial effect of Nd:YAG lasers on the regeneration of bone defects which were left empty or filled with collagen sponge, suggesting its great potential in postoperative treatment targeting local bone healing.