We evaluated the biocompatibility of resin-based root canal sealers (RCSs) in the periapical tissues of rats. Wistar rats underwent tooth replantation for reproducing the response of periapical tissue with RCSs. The resin-based Epipany SE™, AH Plus Jet™, the eugenol-based sealer (Canals) and a control group were employed. The upper right first molar was extracted and applied with RCSs on apices, and then the tooth was repositioned. Histological evaluation demonstrated that mild inflammation occurred in the periapical tissue with Epiphany and AH Plus Jet sealers on day 7, whereas Canals induced severe-to-moderate inflammation. The statistical analyses demonstrated that the significant differences were observed between Canals and the other groups on day 7 regarding inflammatory response. On day 14, the lesions induced by all sealers were healed and replaced predominantly by fibrous connective tissue. Our results suggest that Epiphany SE and AH Plus Jet are good biocompatible materials.