We have previously developed a computer-aided system for examination of the three-dimensional bone structure around implants and observed the bone changes in the healing period after implant placement. This paper describes the bone changes around hydroxyapatite (HA) and titanium (Ti) implants after abutment placement using histological and three-dimensional examinations. Twenty-four HA and Ti implants were embedded in the tibias of adult male New Zealand white rabbits. After 8 weeks, the abutment had passed through periosteum and was placed under the skin. Rabbits were sacrificed 4 and 8 weeks following abutment placement. In conclusion, histological examination showed that, at 4 weeks after abutment placement, bone resorption around the implant neck was seen in both HA and Ti implants, and at 8 weeks, excessive bone formation was seen around the implant neck. Three-dimensional bone examination showed that abutment placement may affect bone formation and cause additional bone hypertrophy in the bone marrow area.