An apicoectomy is a procedure in which the endodontist opens the gum tissue near the tooth to see the underlying bone and remove any inflamed or infected tissue. The very end of the root is also removed. An apicoectomy may be needed when an infection develops or persists after root canal treatment or retreatment. During root canal treatment, the canals are cleaned, and inflamed or infected tissue is removed.

Root canals are very complex, with many small branches off the main canal. Sometimes, even after root canal treatment, infected debris can remain in these branches and possibly prevent healing or cause re-infection later. In an apicoectomy, the root tip, or apex, is removed along with the infected tissue. A filling is then placed to seal the end of the root.