Purpose: This study compared the bone regeneration response of different bone graft materials inside canals within anodized titanium implants in cortical and cancellous bone. Materials and Methods: Upper and lower transverse canals were created in anodic oxidized-surface titanium implants to serve as sites for cortical and cancellous bone regeneration, respectively. The canals were filled with bone graft materials- rabbit bone marrow-derived mesenchymal stem cells and platelet-rich plasma, xenograft, or alloplast (micromacroporous biphasic calcium phosphate)-or left empty (as a control). Eighty implants were surgically placed into the tibiae of 20 New Zealand white rabbits. After 4 and 12 weeks of healing, histomorphometric analysis was performed to measure the newly formed bone areas (NBs) inside the canals. Results: Inside the upper canals, the bone graft groups provided significantly higher NBs than the control (no graft). However, there was no significant difference in NBs between the bone graft groups. Inside the lower canals, no significant difference in NBs was shown among the all groups. The NBs inside the upper canals were significantly greater than those inside the lower canals in all groups after 4 and 12 weeks, respectively. Conclusions: In the cortical bone, there was significant difference in bone regeneration between the control and the bone graft groups. However, there was no significant difference among the bone graft groups in cortical and cancellous bone regeneration. There was significant difference in bone regeneration between the cortical and cancellous bone regions in the all groups using the titanium canal model. Keywords: bone graft material, bone regeneration, mesenchymal stem cell, tissue engineering, implant canal model