The aim of this study was to evaluate and compare Biodentine and Mineral Trioxide Aggregate (MTA) in terms of cytotoxicity and sealing ability when used as a furcation perforation repair materials.For Cytotoxicity test, cultured BHK cells were treated directly by fabricated discs of the Biodentine and MTA and indirectly through adding four different concentrations of extracts from immersion of discs of set materials in culture medium for 2 and 7 days. Cytotoxicity was evaluated by MTT test.For sealing ability evaluation, thirty extracted human permanent mandibular first molars with and non fused roots were used in this study. After access cavity preparation, canals were located and enlarged using Gates Glidden, then flowable composite was used to seal the canals as well as the root apices to prevent coronal and apical leakage through the canals. Teeth were then covered by a double coat of nail polish and perforations were made in the furcation area using size 2 round bur. Teeth were randomly distributed into two experimental groups (n= 10) for each according to the perforation repair material and two control groups (n= 5) for each:•Group (A): where Biodentine was used to seal the perforation.•Group (B): where MTA was used to seal the perforation.•Group (C): positive control, teeth with perforation but without repair material.•Group (D): negative control, teeth with no perforation.Access cavities were sealed using temporary filling then teeth were placed in a 50 % weight AgNO3 dye solution for 4 hours in dark so that the dye covered the roots as well as up to 4 mm above the furcation area then, rinsed in distilled water then immersed in quick photographic film developing solution for 4 hours under light. Teeth were sectioned longitudinally parallel to the long axis of the tooth through the repaired perforation using safe sided diamond disc. Finally, each section was examined under stereomicroscope for detection of dye penetration at X20. Results for cytotoxicity test revealed that; in direct contact, Biodentine group showed higher cellular proliferation than the controls and MTA groups when placed in direct contact with the cells. While in indirect contact, both Biodentine group and MTA group at 2 and 7 days observation periods, acted in a similar pattern, where; 1/2 concentration had highest cell survival percentage indicating cellular proliferation at such concentration. Full concentration had a marked decreased proliferation of cells suggesting cytotoxicity at high levels. In addition, 1/4 and 1/8 concentrations cells survival rate were no different than blank control. Regarding sealing ability, results showed that both perforation repair materials MTA and Biodentine were effective in sealing the furcation perforations when compared to the positive control group. Yet, MTA showed higher mean leakage percentage than Biodentine, indicating better sealing ability and good marginal integrity of Biodentine.