Hydrothermal processing plays a key role in the synthesis of biomaterials with excellent biocompatibility in the physiological environment. Especially, calcium phosphates are paid to much attention for the regenerative medicine. Two kinds of porous materials of hydroxyapatite with 70% porosity were prepared. One of them is a newly developed calcium-deficient hydroxyapatite composed of rod-shaped particles of about 20 μm in length synthesized hydrothermally (HHA) and the other one is the stoichiometric hydroxyapatite (SHA) prepared by the conventional sintering method. These materials were used for animal implantation tests to compare these biological responses. In the rabbit femur, implanted HHA was slowly resorbed and then most of the implanted HHA was resorbed after 72 weeks. The implanted SHA was unresorbed throughout the experimental period. The volume of newly formed bone and the number of osteoclasts in the implanted region were significantly larger in HHA than in SHA after 24 weeks. Results in the present research suggested that the activity of osteoclasts correlated to the bone forming activity of osteoblasts. The method to synthesize biodegradable pure calcium-deficient HA is expected to provide adequate biodegradability and bone replaceability.