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This study aimed to evaluate one-year radiographic healing after endodontic microsurgery using CBCT with modified PENN 3D criteria and to compare the outcome with results evaluated using Molven&rsquo, s criteria. A total of 107 teeth from 96 patients were evaluated one year after endodontic microsurgery by using CBCT scans with modified PENN 3D criteria and periapical radiographs with Molven&rsquo, s criteria. Both preoperative and postoperative lesion volumes were calculated using ITK-SNAP (free software). Radiographic healing assessment using periapical radiographs and CBCT images, and preoperative and postoperative lesion volume measurements were performed independently by two examiners. The assessment using Molven&rsquo, s criteria resulted in 75 complete healings, 18 incomplete healings, eight uncertain healings, and six unsatisfactory healings. Based on modified PENN 3D criteria, 64 teeth were categorized as complete healing, 29 teeth as limited healing, six teeth as uncertain healing, and eight teeth as unsatisfactory healing. With the one-year follow-up, CBCT scans showed a lower healing tendency than did periapical radiography. The volumes of apical radiolucency after the surgery were reduced by 77.7% on average at one-year follow up.