The treatment of vertical bone defects caused by severe periodontal disease requires the regeneration of periodontal tissue. Although various bone substitutes have been clinically applied to vertical bone defect correction, the evaluation of these materials in periodontal tissue remains incomplete. The purpose of this study was to examine the bone regeneration abilities of various bone substitutes including Cytrans, Cerasorb, Neobone and Bio-Oss in a 3-wall bone defect animal model. All of these bone substitutes showed a similar healing ability to periodontal ligament and cementum. However, Cytrans showed the fastest bone healing ability compared with the other materials at 4 weeks post-transplantation. In addition, the recruitment of osteoclasts and endothelial cells was observed in Cytrans grafts at 4 weeks, but only detected at 8 weeks in the other materials. These results suggest that Cytrans promotes faster bone healing by inducing bone remodeling and angiogenesis.