OBJECTIVE This study evaluated the treatment outcome after periapical surgery with the use of 2 different retrograde root-filling materials and the influence of 3 pre- and perioperative variables on the periapical healing. METHODS Two hundred six teeth in 164 patients were randomly allocated to receive either IRM or Super-EBA as a retrograde root-end seal. The teeth were reviewed 12 months after surgery. The influence of lesion size, lesion type, and orthograde root filling quality on healing was analyzed. RESULTS One hundred ninety-four teeth in 153 patients were reviewed. Radiologic evaluation and clinical examination revealed 91% success rate for the IRM group and 82% for the Super-EBA group. There was no statistical significance in the healing outcome between the 2 groups (Fisher exact test). The analyzed pre- and perioperative variables had no significant influence on the treatment outcome (Z test). CONCLUSIONS Both retrograde materials tested in this study can serve as a root-end seal in periapical infected teeth, according to the results of the healing outcome after 12 months' follow-up.