Objective: To evaluate the healing events in degree III furcation defects in dogs following the application of the combination of an enamel matrix derivative with a biphasic calcium phosphate (Emdogain Plus). Method and Materials: Seventeen degree III furcation defects, 5 mm high and 4 mm wide, were created in 9 dogs. In both groups, the defects were conditioned with EDTA. One defect was treated with Emdogain Plus (n = 9), while the contralateral defect serving as control remained empty (n = 8). The defects in both groups were fully covered by coronally repositioned flaps. After 5 months of healing, histologic and histometric analysis was preformed. Results: A significant amount of new attachment and bone formation was observed in both control and test specimens. However, in a number of control specimens, ankylosis was also observed. In the control and test groups, respectively, the mean new cementum length was 10.8 ± 2.1 mm and 8.6 ± 3.2 mm; the mean periodontal ligament length was 7.6 ± 3.8 mm and 8.1 ± 4.0 mm. The mean new bone height was 4.4 ± 1.3 mm and 4.3 ± 1.6 mm in the control and test groups, respectively. No statistical differences were found between the two groups in terms of amount of cementum, periodontal ligament, and alveolar bone regeneration. Conclusion: The present study failed to show higher amounts of newly formed cementum and bone following treatment of acute degree III mandibular furcation defects following use of Emdogain Plus compared with a coronally advanced flap. Emdogain Plus seems to have a protective role against ankylosis in this type of defect. Keywords: enamel proteins, furcation, periodontal regeneration