The aim was to evaluate histologically the inflammatory reactions and tissue responses to an experimental tricalcium phosphate cement (TCP) and mineral trioxide aggregate (MTA) when used as repair materials in furcation perforations in dogs. Perforations were performed in 24 mandibular premolars of six anaesthetised dogs and filled either with ProRoot MTA (grey) or TCP. The root canals were subsequently shaped and filled, and the access cavities were closed with a bonded composite resin. The animals were killed at 12 weeks. After radiological examination, the teeth and surrounding structures were processed for light microscopy. Concerning the grades of inflammation, MTA exhibited significantly better results than TCP (chi-square test according to Pearson). No furcation was free of inflammatory cells. Mild inflammation was observed in nine of twelve cases with MTA and only twice in those with TCP. No significant differences were revealed between MTA and TCP in terms of bone reorganization or deposition of fibrous connective tissue (Mantel-Haenszel chi-square test). The grade of radiological examination corresponded with the grade of inflammation or differed by only one grade plus or minus. Perforations located in the furcation of teeth remain an endodontic and a periodontal problem with an uncertain prognosis, in spite of the promising modern materials applied.