Purpose: The purpose of this retrospective clinical study was to monitor the outcomes of periapical surgery in periapically infected tooth with or without retrograde filling materials (MTA or IRM). Patients and Methods: A total of 85 teeth in 63 patients were included in the study between November 2004 and August 2008. Randomly, MTA or IRM was used as a retrograde filling material or only apical resection without retrograde filling. Teeth with advanced periodontal bone loss or presence of root fracture were excluded from the study. The patients were subjected to a minimum follow-up period of 12 months, with a mean of 17.1 months. Results: Successful healing was observed in 83.3% of the MTA-treated teeth, 80% of the IRM-treated teeth and 75% of the teeth which was not retrograde filling. Doubtful healing was seen 9.3% (MTA), 13.3% (IRM), 12.5% (no retro-filling). The success rate of upper incisors (92%) was higher than lower lincisor and molars (66.7% and 50%, respectively). Conclusion: In this study, periapical surgery including retrograde filling improves the prognosis. And, no statistically significant differences were found between retrograde filling materials (MTA or IRM).