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Root canal treatment may not save a tooth when it fails to heal or becomes painful or diseased months or even years later. The tooth may have a tiny fracture or a canal that could not be detected during treatment. Calcification (calcium deposits) may make a canal too narrow for the cleaning and shaping instruments used in nonsurgical root canal treatment to reach the end of the root. Inflammation or infection may persist in the bony area around the end of the tooth after a root canal procedure.

These situations may require surgery to locate fractures or hidden canals that do not appear on x-rays but still cause pain in the tooth or to treat damaged root surfaces or the surrounding bone. The most common surgery used to save damaged teeth is an apicoectomy or root-end resection.

In an apicoectomy the endodontist makes an incision in the gum tissue to expose the bone and surrounding inflamed tissue. Damaged tissue is removed along with the end of the root tip. The endodontist places a root-end filling to prevent reinfection of the root and sutures the gum. The bone naturally heals around the root.