Aim: The first aim of this study was to evaluate the healing outcome after periapical surgery performed using an ultrasonic cleaning technique in conjunction with the use of either Intermediate Restorative Material (IRM) or mineral trioxide aggregate (MTA) as a retrograde root-end seal in teeth with apical periodontitis. A second aim was to determine if the type of coronal restoration had any impact on the healing outcome. Methodology: One hundred eighty-six consecutive teeth in 177 patients referred for periapical surgery were randomly allocated into two parallel groups, receiving either IRM or MTA as a retrograde root-end seal. The patients were reviewed 12 months after surgery. Fisher's exact test and Z-test analysis were performed. Results: One hundred sixty-six teeth in 158 patients were reviewed 12 months after surgery. Radiological evaluation and clinical examination revealed an 86% success rate for the IRM group and 85% for the MTA group. There was no statistically significant difference (p=0.829) between the two groups regarding the healing outcome (Fisher's test). The type of coronal restoration (p=0.575) had no impact on the healing outcome (Z-test). Conclusions: The tested materials, IRM and MTA, are both suitable as retrograde root-end filling materials in conjunction with an ultrasonic root-end preparation technique according to the results at the 12-month follow-up. The results of this study also show that the type of coronal restoration had no impact on the healing outcome following periapical surgery.