Statement of the Problem: Different materials have been used to repair Root perforations, the most successful of which is mineral trioxide aggregate (MTA). It is technically difficult to use MTA for perforation repair. Recently, some bio-ceramic sealers such as Endoseal MTA were introduced to repair the perforation site during Root filling, which decreases the technical difficulty of this Procedure. Purpose: The aim of this study was to compare the bacterial microleakage of Pro-Root MTA and Endoseal MTA sealer in Root perforation repair. Materials and Method: This in vitro experimental study evaluated 40 extracted canine teeth. After Root canal cleaning and shaping, a Root perforation was artificially created at 7 mm below the cementoenamel junction. The teeth were then randomly divided into two ex-perimental groups (n=18) of Pro-Root MTA and Endoseal MTA, and two positive and nega-tive control groups (n=2). Perforation sealing and Root canal filling were performed in the two experimental groups according to the manufacturers’ instructions. After sterilization of the whole system with gamma ray, microleakage was tested using a double-chamber model. Data regarding the presence/absence of microleakage were reported after 35 days. The data were analyzed by SPSS software using the Chi-square test. Results: There was no significant difference between the two experimental groups regarding bacterial microleakage (p> 0. 05). Conclusion: Under the conditions of this study, it can be concluded that the sealing ability of perforation repair with Endoseal MTA Sealer and Pro-Root MTA was comparable.