Periapical surgery is now a reliable therapeutic procedure for the treatment of teeth with periapical lesions, particularly when orthograde retreatment is problematic. However, little information is available regarding treatment planning of cases referred for periapical surgery. Therefore, this study was conducted to analyze and evaluate the factors that affect the decision-making process for periapical surgery. This study retrospectively assessed clinical and radiographic data from patients undergoing periapical surgery. The factors involved in deciding to perform periapical surgery were classified into technical, biological, and combined factors. Out of 821 patients, 544 (66.3%) underwent endodontic treatment/retreatment, 204 (24.8%) were treated with coronal restorations and 60 (7.3%) were treated with post. Periapical surgery was indicated for biological reasons in 35% of patients and for technical reasons in 17.9%. The common biological factor was persistent clinical symptoms (19.7%). The most common technical cause was failure of previous endodontic treatment (66.3%). Nearly half of all periapical lesions (45%) were <5 mm in size. Periapical surgery was justified in only 434 (52.9%) subjects. We suggest that it is very important for patients to be informed and encouraged about endodontic retreatment in order to reduce unnecessary surgical procedures.