BACKGROUND Long-term success of endodontic surgeries is often influenced by the type of root-end filling material (RFM). The aim of present study was to compare the marginal adaptation of two different RFM, cold ceramic (CC) and mineral trioxide aggregate (MTA), using scanning electron microscope (SEM). METHODS About 20 extracted human single-rooted teeth were collected and stored into sodium hypochlorite 5.25%. The teeth were decronated from the cemento-enamel junction to prepare 16 mm roots. The working length was measured, and 1/3 coronal of the canal was prepared by Gates-Glidden drills. Apical flaring was followed by K file size # 40-70 based on step back technique. After filling of the canals, 3 mm above the apex was cut at 90° to the long axis. Furthermore, 3 mm of the filling was removed from the apical part using the ultrasonic device. All of the prepared specimens were divided into two groups and were retro filled by MTA and CC. The roots were cut horizontally from 1 mm above the apical part, and dentin-filling material interface was observed by SEM. Finally, the collected data were analyzed by Mann-Whitney test and using SPSS software version 18 at a significant level of 0.05. RESULTS The mean interfacial adaptation was higher in CC group. However, no significant differences were observed by statistical test (P = 0.35). CONCLUSIONS Both CC and MTA had similar marginal adaptation as RFM however in vivo studies are recommended for better determination.