The prognosis of transplanted teeth is strongly related with periodontal healing. Several experimental studies showed that the application of enamel matrix derivatives on periodontitis-affected root surfaces resulted in periodontal regeneration. The purpose of this study was to determine the effect of enamel matrix derivatives on periodontitis-affected root surfaces prior to transplantation in dogs. Class III Furcation defects were surgically created on the left second, the third and the fourth premolar in the mandibles of nine mongrel dogs and experimental periodontitis was induced by placing small cotton pellets into defects for 3 weeks. Periodontitis-affected roots were treated by scaling and planing and the coronal portions were removed. Each root was extracted and implanted into recipient bed prepared in the contralateral premolar area. The transplanted roots were grouped according to the treatment modalities; Group I- roots treated with saline only, Group II- roots conditioned by neutral EDTA, and Group III- roots conditioned by neutral EDTA and enamel matrix derivatives ($EMDOGAIN^{(R)}$, BIORA Co., Sweden). The animals were sacrificed at 1 week, 3 weeks, and 10 weeks after transplantation and decalcified specimens were prepared for histologic examination. In Group I, healing was most frequently characterized by root resorption and ankylosis. In Group II, with root resorption and ankylosis in a few specimens, connective tissue attachment was partly seen on denuded root surface, but no cementum formation was seen. In Group III, there was regeneration by new cementum and periodontal ligament on denuded root surface, although slight root resorption and ankylosis were found in a few specimens. This result suggests that enamel matrix derivatives treatment on periodontitis-aggected root surface could reduce the frequency of root resorption and ankylosis and contribute to periodontal regeneration, and might be useful for autologous transplantation.