This study evaluated the effect of 980-nm diode laser on apical microleakage and intraradicular dentin morphology. Roots of 110 mandibular incisors were used in the study: 92 for microleakage test and 18 for scanning electron microscopy (SEM). Roots were randomly assigned to 3 groups according to the irrigating solution (water, NaOCl and NaOCl/EDTA) and were divided into 3 subgroups according to the laser irradiation protocol (without irradiation, irradiated at 1.5 W and irradiated at 3.0 W). Two specimens of each subgroup were prepared for SEM. The remaining roots were filled with AH Plus and gutta-percha. Apical leakage was assessed by ink penetration and data were analyzed statistically by ANOVA and Tukey-Krammer test (α=0.05). SEM analysis showed intensification of changes with increase of laser power as well as variations according to the irrigating solution. Modified smear layer was observed in specimens treated with water and irradiated with laser. Roots irrigated with NaOCl/EDTA had lower levels of infiltration (0.17 ± 0.18 mm) differing significantly (p<0.05) from those of roots irrigated with water (0.34 ± 0.30 mm), but similar (p>0.05) to those irrigated with NaOCl (0.28 ± 0.29 mm). Non-irradiated roots had lower levels of infiltration (0.10 ± 0.14 mm), differing (p<0.05) from those irradiated at 1.5 W (0.32 ± 0.22 mm) and 3.0 W (0.37 ± 0.32 mm). The 980 nm diode laser modified dentin morphology and increased apical microleakage.