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The present study was undertaken for evaluating the sealing ability of furcation repair materials GC Fuji VII, MTA Plus and Biodentine. Diagnosis of iatrogenic perforation requires a combination of symptomatic findings in clinical observations. Perforations can be defined as mechanical or pathological communications between the root canal system and the external tooth surface. Study was conducted in the Department of Conservative Dentistry and Endodontics, Himachal Dental College, Sundernagar, Himachal Pradesh, India. Fifty five sound mandibular molars with non fused and well developed roots were used for the study. The specimens were examined using SEM which is maintained approximately 15Kv and 10-6 Torr under high vacuum condition. Specimen imaging were done by secondary electrons using a secondary electron detector. Scanning Electron Microscope (SEM) pictures, MTA plus shows the minimum marginal gap of 2.17 micrometers, followed by Biodentine 5.55 micrometers and GC FUJI VII 8.00 micrometers. The most important factors determining the success of a perforation repair procedure are the location of the perforation; time elapsed between the occurrence of the perforation and repair, the ability of the material to seal the perforation and the biocompatibility of the repair material. In our study, MTA Plus showed minimum leakage compared to GC FUJI VII and Biodentine. The minimum microleakage as observed in MTA Plus group might be attributed to its superior marginal sealing ability resulting from its hydrophilic properties and formations of an inter facial layer. Biodentine also provides a good seal almost similar to that of MTA Plus when used as a furcation repair material. GC Fuji VII showed significantly more leakage and gap formation than Biodentine and MTA Plus.