Autogenous bone grafts have frequently been used in the treatment of bone defects; however, this procedure can cause clinical complications after surgery. Besides, the amount of available bone is sometimes insufficient. Therefore, synthetic biomaterials have been researched as an alternative to autogenous bone graft implants. The objective of this study was to evaluate the repair of bone defects treated with compact autogenous bone graft or porous calcium phosphate ceramics. Three defects 3 mm in diameter were produced in the skull of 21 rats. One the defects was produced in the frontal bone, which remained empty, while the others were produced in the right and left parietal bones, which were filled respectively with ceramics and autogenous bone graft. The animals were sacrificed 1, 2, 4, and 24 weeks after surgery and analyzed by light microscopy and radiography. In the twenty-fourth week, the defects filled with autogenous bone graft and ceramics had similar volumes of newly formed bone tissue. The ceramics offered favorable conditions to bone tissue growth. Thus, we concluded that the calcium phosphate ceramic implant proved to be effective in repairing defects produced in the skull of rats.