Introduction: The aim of this study was to investigate the outcome of endodontic microsurgery and analyze the prognostic factors. Methods: Our prospective cohort study included 98 teeth in 81 patients. An endodontist performed all surgical procedures using endodontic microsurgical approaches. The treated teeth were recalled and examined clinically and radiographically at least 1 year after surgical treatment. The outcome was determined based on clinical and radiographic results. Radiographic healing was classified into 4 categories: complete, incomplete, uncertain, and unsatisfactory healing. An analysis of predictors was performed using multi-variate logistic regression. Results: At recall, 74 of the 98 teeth (75.5%) were examined 12 to 30 months after surgery; 71 of the 74 teeth were analyzed clinically and radiographically, and 3 teeth had been extracted. On periapical radiographs, 55 (74.3%) of the 74 teeth showed complete healing, whereas 12 (16.2%) demonstrated incomplete healing. Together the percentage of complete and incomplete healing was 90.5% (67/74), and all 67 teeth were clinically normal. Uncertain healing was observed in 3 teeth (4.1%), one of which was symptomatic with swelling and sinus tract involvement and the other 2 were asymptomatic. The remaining 1 tooth (1.4%) showed unsatisfactory healing and was asymptomatic. The use as an abutment was found to be a negative factor associated with patient outcome (P<.05; odds ratio = 22; confidence interval, 20.47-23.53). Conclusions: The combined rate of complete and incomplete healing of teeth 12 to 30 months after endodontic microsurgery was 90.5%. The use as an abutment may have a negative effect on treatment outcome. (J Endod 2017;43:694-698)