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Introduction: Furcation perforation is one of the complications that occur during endodontic treatment due to anatomical differences or iatrogenic causes. Repairing the perforation with a bio-compatible material eliminates the connection with the gingival sulcus and positively affects the prognosis. The sealing ability of the repair materials is very important and is affected by the conditions of the environment in which they are applied. Aim: To compare the sealing efficiency of Mineral Trioxide Aggregate (MTA) (Angelus, Londrina, PR, Brazil) and Biodentine (Septodont, Saint Maur des Fosses, France) materials used in the repair of furcation perforations in acidic and neutral environments. Materials and Methods: This in-vitro experimental study was carried out in the Department of Endodontics at Dicle University Faculty of Dentistry, Diyarbakır, Türkiye and Dicle University Science and Technology Application and Research Center from 10th June 2020 to 22nd July 2020. A total of 96 mandibular molars were used in the study. The specimens were randomly divided into two equal groups (n=48). When the perforations were repaired with MTA and Biodentine materials, each group was divided into four subgroups (n=12). These subgroups were kept in Phosphate-Buffered Saline (PBS) and Acetic Acid (AA) solutions for different periods of time from four or 34 days, and all groups were immersed in methylene blue solution. The dye penetration level of the divided sections was examined under a stereomicroscope (Leica, Wetzlar, Germany). Microleakage data of all groups were statistically analysed using Kolmogorov Smirnov, Shapiro Wilk's and Mann-Whitney U Test. Statistical significance was set at 0.05, it was stated that there was a significant difference when p-value <0.05. Results: The short-term (4 days) microleakage level of biodentine material in the AA environment was significantly lower than that of MTA material (p-value=0.005). There was no statistically significant difference between the materials in terms of long-term (34 days) microleakage levels in the AA environment (p-value>0.05). The long-term microleakage level in PBS environment of biodentine material was significantly lower than that of the AA environment (p-value=0.008). Conclusion: Lower microleakage levels were observed in the neutral environment than the acid environment with both MTA and biodentine during both holding periods. [ABSTRACT FROM AUTHOR]