This study assessed the 5-year outcome of apical microsurgery in 170 teeth from 191 subjects who underwent the procedure. At the 5-year follow-up, 129 teeth (75.9%) were healed compared to 83.8% at 1 year. Two significant predictors of healing outcome were identified: teeth with interproximal bone loss >3 mm from the cementoenamel junction had a lower healing rate (52.9%) compared to those with ≤3 mm bone loss (78.2%); and teeth filled with ProRoot MTA had a higher healing rate (86.4%) than those filled with SuperEBA (67.3%).