Modern surgical endodontics is an efficient and predictable treatment for teeth with apical periodontitis; however, like any treatment modality, it is exposed to the risk of complications. This chapter presents a review of potential foremost clinical complications, including soft and hard tissue complications that may occur during the surgery or at the postoperative period. A clinician should always be actively prepared to prevent and manage any complications of the surgical procedure. Careful and adequate treatment planning and surgical technique, knowledge of the relevant anatomy, and a thorough anamnesis should be incorporated in the daily practice for the prevention and management of surgical complications.