Introduction: The purpose of this study was to determine the bone regeneration potential to different root-end filling materials by evaluating the distance between the materials and newly regenerated bone after root-end surgery. Material and Methods: Periapical lesions were induced in premolars and molars of five female beagle dogs. The teeth were treated endodontically after the development of the lesions. After 1 week, the teeth underwent root-end surgery using modern microsurgical techniques. Three different root-end filing materials were used: amalgam (Tytin; Kerr Mfg Co, Romulus, MI), SuperEBA (Bosworth, Skokie, IL), and mineral trioxide aggregates (MTA; Dentsply, York, PA). After 4 months, the dogs were sacrificed, and the jaws were prepared for histological sectioning. The distances from the root-end filling materials to the regenerated bone were determined by the evaluation of microradiographic images of the sections with imaging software (Sigma Scan/Image; Jandel Scientific Software, San Rafael, CA). The results were statistically analyzed with analysis of variance using Sigma Stat software (Jandel Scientific Software, San Rafael, CA). Results: The mean distances from the newly regenerated bone were 0.397 +/- 0.278 mm in the MTA group, 0.756 +/- 0.581 mm in the SuperEBA group, and 1.290 +/- 0.386 mm in the amalgam group. There was a statistically significant difference between the amalgam and MTA groups (p < 0.05). No significant differences existed for amalgam versus SuperEBA and SuperEBA versus MTA. Conclusion: MTA showed the most favorable periapical tissue response. The distance from MTA to the regenerated bone was similar to the normal average periodontal ligament thickness in dogs. (J Endod 2010;36:1323-1325)