Background: Furcal perforation is one of the reasons for endodontic treatment failure, and repairing it is a challenge. Studying new repairing materials, as opposed to conventional White -Mineral trioxide aggregate (MTA) contributes to the success of the endodontic treatment. Objectives: to evaluate the sealing ability of nano-hydroxyapatite and nano-MTA as a repair material for bifurcation perforation compared to conventional MTA. Materials and methods: Fifty extracted human mandibular lower permanent molars with intact furcation area were randomly distributed into five groups: negative control group without perforation (n=10), positive control group where the perforation is unrepaired (n=10), and three groups according to the perforation repair material used with (n=10 for each); Group A: nano-sized Hydroxyapatite, Group B: nano-sized MTA and Group C: conventional MTA (ProRoot MTA). Perforation was created in the bifurcation area, then repaired using the three materials. Dye extraction method with spectrophotometer UV used for sealing ability evaluation. Results: there is a statistically significant difference in results between all repair materials used. Conclusion: Nano-MTA showed promising results in compassion with Conventional MTA (ProRoot MTA).