Introduction: This retrospective study assessed the effects of microsurgical treatment of post-treatment endodontic disease using SuperEBA (Bosworth, Skokie, IL) as the root-end filling material and evaluated the potential prognostic factors in relation to outcome. Methods: Data were collected from patients diagnosed with post-treatment endodontic disease who then underwent endodontic microsurgery between April 2007 and October 2010. The effect was evaluated 2 years after the operation. Surgical procedures were performed by a single endodontic specialist. After surgery, operation records were recorded including preoperative, intra-operative, and postoperative factors from the clinical and radiographic measures. For statistical analysis of the predisposing factors, the dependent variable was the dichotomous outcome (ie, success vs failure). Results: Eighty-two patients with 101 treated teeth met the inclusion criteria. The recall rate was 87.2%. Of these microsurgically treated cases, the overall healing rate was 93.1%. At the 0.05 significance level, age, sex, tooth position, size of periapical radiolucency, biopsy result of periapical lesion, and presence of a sinus tract appeared to have no significant effects on the outcome (P>.05). Conclusions: Microsurgical endodontic treatment using SuperEBA as the root-end filling material is a favorable option for post-treatment endodontic disease.