Objective: To assess the influence of root-end filling (REF) material on apical surgery outcome. Materials and methods: Cases of apical surgery performed in a private practice limited to endodontics, which had received Intermediate Restorative Material (IRM; Group 1) or mineral trioxide aggregate (MTA; Group 2) as the REF material were collected. Radiographic surgical healing at up to 12 months and 24 months was evaluated using agreed criteria by two trained observers. The results were analysed using the Pearson chi-square and Fisher exact tests, with the level of significance set at P 0.05. Results: Twenty-two out of the 95 teeth were excluded for various reasons leaving a total of 73 teeth. Group 2 showed a significantly higher healed rate than Group 1 (81% vs 56%; P = 0.0189); however, the difference between 'healed' and 'healing' teeth was not statistically significant for both follow-up periods (≤ 12 months, P = 0.2852; ≤ 24 months, P = 0.1101). As a secondary observation, it was found that 'large' lesions (> 5 mm diameter) required a longer time to heal than 'small' lesions (48% vs 77%; P = 0.0147). Analysis of the REF material in relation to lesion size showed that MTA 'healed' rates were significantly higher for 'small' lesions than 'large' lesions (P = 0.0042), whereas with IRM, the difference was insignificant (P = 0.4217). Conclusions: MTA showed a higher rate of 'complete healing'. 'Large' lesions took a longer time to heal completely. 'Small' lesions had a higher 'healed' rate when MTA was used as the REF material. Keywords: apical surgery, Intermediate Restorative Material, mineral trioxide aggregate, outcome, root-end filling