Abstract: Objective: To compare the prognosis assessment of endodontic microsurgery treatment for beagle dogs' experimental periodontitis between cone beam CT (CBCT) and periapical radiographs (PRs). Methods: Pulps of 18 premolars in 3 beagle dogs were exposed to oral environment for 8 weeks. All 36 roots of the premolars developed apical periodontitis confirmed by both PRs and CBCT. All teeth received root canal treatment, followed by endodontic microsurgery. PRs and CBCT were performed both immediately and 6 months after endodontic microsurgery. The ability to detect periapical bone defect was compared accroding to apical radiolucent lesion area on the radiographic films of two methods. Results: Immediately after endodontic microsurgery, the areas of apical radiolucent lesions in both CBCT sagittal and coronal plane were greater than those in PRs (P=0.000, P=0.026). There was no significant difference between CBCT sagittal and coronal plane (P=0.070). 6 months after endodontic microsurgery, the area of apical radiolucent lesions in both CBCT sagittal and coronal plane were greater than those in PRs (P=0.000, P=0.012). The area of apical radiolucent lesions in CBCT sagittal plane was significantly greater than that in coronal plane (P=0.001). Conclusion: CBCT is better than PRs in detecting periapical bone defect, and can serve as an effective evaluation method in the evaluation of endodontic microsurgery.