Introduction: Quality endodontic surgical treatment is directly related to correct incision planning, flap design, root end resection and retro filling. Biodentine, a calicium silicate based cement, is biocompatible and bioactive with improved handling properties and is supposed to be a good retrofilling material and is comparative with other root endo restorarive material like MTA. It has better handling which is of importance during endodontic surgery. Objective: Comparative evaluation of the marginal adaptation of biodentine, mineral trioxide aggregate(MTA) and glass ionomer cement as root end filling materials. Materials and Methods: The study has been carried out on 45 extracted single rooted human teeth (15 for each group). Root canals were cleaned, shaped and obturated using gutta percha and apexit as root canal sealer. After 3mm of root resection, root end cavities of 3mm deep were prepared. 15 samples in each group were root-end filled with biodentine, pro-root MTA and glass ionomer cement and imaged using scanning electron microscope. Results: The SEM microphotographies show Biodentine and MTA both exhibited better marginal adaptation to dentin walls as compared to glass ionomer cement. Conclusion: Biodentine, a newly introduced material showed promising result under scanning electron microscope and is recommended to be tried in vivo. Keywords: retro filling material, biodentine, marginal adaptation