The teeth are held in place by roots that extend into the jawbone. Front teeth usually have one root. Other teeth, such as premolars and molars, have two or more roots. The tip or end of each root is called the apex. Nerves and blood vessels enter the tooth through the apex. They travel through a canal inside the root, and into the pulp chamber. This chamber is inside the crown (the part of the tooth one can see in its mouth).

During root canal treatment, the dentist cleans the canals using special instruments called files. Inflamed or infected tissue is removed. An apicoectomy may be needed when an infection develops or won't go away after root canal treatment or retreatment.

Root canals can be very complex, with many tiny branches off the main canal. Sometimes, even after root canal treatment, infected tissue can remain in these branches. This can possibly prevent healing or cause re-infection later. The dentist can do an apicoectomy to fix the problem so the tooth doesn't need to be extracted. 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.

An apicoectomy is sometimes called endodontic microsurgery because it is often done using an operating microscope.