Background: The aim of this experimental study is to assess the bone healing phenomenon produced in the presence of 3 dental materials used for the root canal obturation. Materials and methods: The biocompatibility of 3 endodontic sealers (a self-curing epoxy resin — AH Plus, a dual cure urethane dimethacrylate resin — RealSeal and a new dual cure endodontic hydroxyapatite based filling material) was investigated after intra-osseous implantation of the materials in rats’ calvaria. Tissue reaction was studied at 2, 4, 6, 8, 10 and 12 weeks after implantation using calibrated image retrieval by Olympus. We took into consideration the presence of inflammatory cells (polymorphonuclear leukocytes, macrophages, plasma cells, lymphocytes and giant cells) and classified the aspects of the histological samples according to the following scale: 0 — no inflammation, 1 — mild, isolated inflammation, 2 — moderate, localised inflammatory reaction, 3 — severe, diffuse and intense inflammatory reaction. Results: The inflammatory reaction was present at the 6 intervals for all the tested materials, but a decrease of the inflammatory infiltrate, statistically significant, until extinction for all tested materials was observed at the end of the experimental period. The reaction of bone tissue recovery was most intense in the case of the control area. Lower intensity osteogenesis phenomenon was observed in case of all 3 tested sealers at the end of the experimental period. Conclusions: Biocompatibility and bone healing induction of the new hydroxyapatite based endodontic filling material is comparable to other commercial materials, AH Plus and RealSeal. (Folia Morphol 2016; 75, 1: 14–20)