X-rays usually show an unresolved, black circle around the tooth long after the initial root canal was performed. Sometimes a fistula, (which looks like a pimple) might be present in the gum, or swelling and pain may be present.

The goal of the procedure is to remove the root tip (apex) of the tooth and the surrounding infected tissue.

After an injection of local anesthetic, the gum is lifted to expose the root end of the tooth. This root end is then removed along with all of the surrounding infected tissue. A root-end filling is placed to seal the end of the root. Without proper sealing of all the canals present in the tooth, the apicoectomy will not be successful. Often, the end of the root develops a cyst which is removed together with the root tip and may require bone grafting for repair. The gum is then re-positioned and a few sutures (stitches) are placed in the gum tissue to ensure proper healing. In a few months, the bone around the tooth has healed and symptoms are gone.