Introduction: Accessing the tooth roots in periapical surgery (PS) requires the elimination of periapical bone. Objective: To compare the postoperative morbidity and prognosis following PS on mandibular molars by ostectomy, or by osteotomy with repositioning of the vestibular cortical. Material and Methods: A retrospective clinical study of mandibular molars subjected to PS with ultrasound. Two groups were considered according to the surgical procedure used to access the roots: Group 1 (G1) with ostectomy and Group 2 (G2) with osteotomy and repositioning of the vestibular cortical. Only patients who had properly followed the post-operative instructions, adequately completed the post-operative questionnaires, and with a minimum of 12 months follow-up were included in the study. Post-operative morbidity was evaluated, and a clinical and radiographic follow-up was carried out using the criteria established by von Arx and Kurt in 1999. The SPSS program version 15 for Windows was used, considering values of p?0.05 as statistically significant. Results: Seventy-five patients, including 18 men and 57 women, with 87 mandibular molars and 107 periapical lesions were subjected to PS. The mean age of the patients was 38.5 years old (range 15 ? 74 years old). The patients were monitored for an average of 27.2 months (range 12 ? 120 months). Sixty-six patients (78 teeth) were treated in G1, and 9 patients (9 teeth) in G2. There was no relationship between the size of the ostectomy and pain, swelling or prognosis (p>0.05). Patients who underwent ostectomy presented more swelling than those subjected to osteotomy (p<0.05). There was no relationship between prognosis and the variables studied (p>0.05). Conclusions: There was no statistically significant relationship between the surgical procedure used and postoperative pain or prognosis. Patients who underwent an ostectomy presented more swelling than those who were treated with an osteotomy and repositioning of the vestibular cortical.