Aim: Although there are many materials that can be used for retrograde filling in surgical endodontics, none of them can be regarded as an ideal material yet. The purpose of this study was to compare the surface topography of three different root-end filling materials. Methods: 36 extracted single rooted human incisor teeth were cleaned and decoronated to standardized 10 mm root lengths. The root segments were prepared and 2 mm apical resection were performed. The samples were randomly separeted to three groups (Group A: Ca(OH)2, Group B: MTA Angelus, Group C: ProRoot MTA), each one of them was comprised of 12 roots. Materials were placed as 2 mm apical barriers and obturated with guttapercha and AH-Plus sealer. Each group was dimidiated into two subgroups (A1,A2,B1,B2,C1,C2). Groups A1,B1,C1 were stored in normal saline (NS), groups A2,B2,C2 were stored in neutral phosphate buffer saline (NPBS) solution and samples were incubated at 370C for 2 weeks. Stereomicroscope (32X) was used to photograph the root-end filling. Results: All specimens demonstrated white crystals formation and sediment over the root-end filling materials and on the superficial border of the root-end cavities’ wall as a white plaque. A2,B2,C2 samples had more crystal sediment on root-end fillings than samples A1,B1,C1. Dissolution and corrosion were observed in groups A1, A2. Conclusions: The results of this study revealed that calcium hydroxide is more resorbable than MTA Angelus and ProRoot MTA. The crystals formation and precipitation were observed in neutral phosphate buffer saline solution which were more than normal saline solution for all groups as a hydroxiapatite crystals.