Introduction Biodentine has been scarcely studied as a furcation perforation (FP) repair material, mostly by in vitro methodologies. This animal study aimed to compare the histological responses, radiographic, and micro-computed tomographic (micro-CT) outcomes after FP repair with Biodentine or ProRoot MTA (MTA) in dogs’ teeth. Methods and Materials Fifty teeth from five dogs were divided into 4 groups: MTA (n=20, FP repaired with ProRoot MTA), BDT (n=20, FP repaired with Biodentine), PC (n=5, positive control, FP without repair) and NC (n=5, negative control, without perforation). The animals were euthanized after 4 months. Histological assessment included inflammatory cell infiltration, hard tissue resorption, hard tissue repair, and cement repair in the furcation area. Immediate postoperative and 4 months follow-up radiographs were compared for radiolucency in the furcation region. The volume of extruded material was quantified using micro-CT images. Results The tested materials showed equivalent radiographic response, together with similar hard tissue resorption and repair but, BDT group showed significantly less inflammation, lower volume of extruded material and higher cement repair than MTA group. Conclusion The outcomes of this study, taken together with other favorable results in literature, are highly suggestive that Biodentine is a promising biomaterial to be used for FP repair.