Purpose: The purpose of this study was to compare the bone regeneration effects of cortical, cancellous, and cortico-cancellous human bone substitutes on calvarial defects of rabbits. Methods: Four 8-mm diameter calvarial defects were created in each of nine New Zealand white rabbits. Freeze-dried cortical bone, freeze-dried cortico-cancellous bone, and demineralized bone matrix with freeze-dried cancellous bone were inserted into the defects, while the non-grafted defect was regarded as the control. After 4, 8, and 12 weeks of healing, the experimental animals were euthanized for specimen preparation. Micro-computed tomography (micro-CT) was performed to calculate the percent bone volume. After histological evaluation, histomorphometric analysis was performed to quantify new bone formation. Results: In micro-CT evaluation, freeze-dried cortico-cancellous human bone showed the highest percent bone volume value among the experimental groups at week 4. At week 8 and week 12, freeze-dried cortical human bone showed the highest percent bone volume value among the experimental groups. In histologic evaluation, at week 4, freeze-dried cortico-cancellous human bone showed more prominent osteoid tissue than any other group. New bone formation was increased in all of the experimental groups at week 8 and 12. Histomorphometric data showed that freeze-dried cortico-cancellous human bone showed a significantly higher new bone formation percentile value than any other experimental group at week 4. At week 8, freeze-dried cortical human bone showed the highest value, of which a significant difference existed between freeze-dried cortical human bone and demineralized bone matrix with freeze-dried cancellous human bone. At week 12, there were no significant differences among the experimental groups. Conclusions: Freeze-dried cortico-cancellous human bone showed swift new bone formation at the 4-week healing phase, whereas there was less difference in new bone formation among the experimental groups in the following healing phases.