The purpose of this study was to compare the effectiveness of mesenchymal stem cells (MSCs) with platelet-rich plasma (PRP) as scaffold and autogenous cortical bone (ACB) graft with and without PRP in the regenerative treatment of class II furcation defects in dogs. The mandibular second, third, and fourth premolars (P2, P3, P4) and maxillary P3 and P4 of both sides in three dogs were selected for experimentation. Class II furcation defects (5 mm in height and 2 mm in depth) were surgically created. Five weeks after the first operation, scaling + root planning (group 1), PRP (group 2), ACB (group 3), combination of ACB/PRP (group 4), and combination of MSCs/PRP (group 5) treatments were performed during open flap debridement. The percentage of cementum and alveolar bone formation was evaluated by histomorphometric analysis after a healing period of 8 weeks. There was new cementum along with periodontal ligament and coronal growth of alveolar bone in all groups. Cementum formation was significantly higher in groups 3, 4, and 5 compared to the control group (P < 0.05) with no significant difference between groups 2, 3, 4, and 5. Alveolar bone formation was similar in all groups (P > 0.05). It can be concluded that periodontal regeneration with complete filling of class II furcation defects with cementum, alveolar bone, and periodontal ligament is obtained 8 weeks after ACB, ACB/PRP, and MSCs/PRP treatments; however, efficacy of none is higher than another.