Purpose: to evaluate the sealing ability of Totalfill^® versus ProRoot MTA in furcal perforations in permanent molars using Scanning Electron Microscopy (SEM). Materials and Methods: Thirty permanent molars were placed in 5% sodium hypochlorite solution and washed with tap water. Access cavities were made using round bur in highspeed handpiece. Perforations were made in the middle of the pulpal floor using size 4 round bur. The teeth were divided into two groups according to the material used to seal the perforation; Group I: ProRoot MTA and Group II: Totalfill^®. The materials were left to set then the samples were sectioned longitudinally and the gap between the material and dentin was measured by SEM. Results: The results of this study showed that Group I (ProRoot MTA) showed more microleakage (17.47 ± 5.58 μm) compared to Group II (Totalfill^®) that showed significantly less leakage (5.28 ± 2.18 μm). Conclusion: Based on the results of this study, it was concluded that Totalfill^® showed better sealing ability and lesser microleakage than that of ProRoot MTA and therefore it can be a good alternative to MTA.