The purpose of this in vitro study was to observe the morphological changes and apical dye penetration at apical dentin surfaces after apicoectomy with conventional techniques and laser beam. Sixty single-rooted extracted teeth were selected for the study. The crowns were resected below the cemento-enamel junction. Then, these teeth were treated endodontically and filled with gutta-percha using AH-26 root canal sealer. The teeth were randomly divided into four groups of 15 teeth in each. The roots were resected perpendicular to its long axis 3 mm from the apex using Er: yttrium-aluminium-garnet (YAG) laser irradiation in groups 1 and 2, and the resected root surfaces were lased with Nd:YAG laser in group 2. The apexes were resected by a high-speed handpiece in groups 3 and 4, and the resected root surfaces were lased with Nd:YAG laser in group 4. Ten teeth in each group were used for leakage studies, and the other five teeth were used for scanning electron microscopic examinations. Seven sections were obtained from each root to assess the microleakage, and the sections were analyzed in a computer-assisted manner. No statistically significant differences were observed between the leakage percentage of groups 1 and 3 and groups 2 and 4 (p>0.05). Morphological differences were observed between apical dentin surfaces resected with conventional techniques and laser beam.