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Background/Purpose: Endodontic microsurgery (EMS) is a reliable treatment for teeth with non-healing apical periodontitis. This study evaluated the outcome of EMS with mineral trioxide aggregate as the retrograde filling material and identified potential prognostic factors associated with the EMS outcome. Methods: Consecutive clinical and radiographic records of EMS performed in a teaching hospital from 2013 to 2017 were reviewed. Cases of root fracture, cemental tear, re-surgery, and incomplete records were excluded. After selection, 268 EMS-treated teeth with the follow-up period more than one year were included. Surgical outcome as success or failure was evaluated according to Molven's criteria. For analysis of potential prognostic factors, multivariate logistic regression was performed followed by bivariate chi-square tests. Stratified analysis was performed to understand the interactions between two prognostic factors. Results: The overall EMS success rate was 89.9% in this study. Tooth type (anteriors vs. molars, odds ratio (OR) = 6.83, P = 0.001, anteriors vs. premolars, OR = 4.27, P = 0.010) and endodontic-periodontal (endo-perio) communicating defects (with vs. without, OR = 4.92, P = 0.005) both had a significant influence on the EMS outcome. The negative impact of endo-perio communicating defects was closely associated with tooth type. Premolars with endo-perio communicating defects had significantly higher rates of failure. Conclusion: The EMS outcome is significantly affected by the tooth type and endo-perio communicating defect. The presence of endo-perio communicating defects has a greater negative influence on the success rate for premolars than for anteriors and molars.