Aim To evaluate ex vivo the effect of Nd:YAG laser irradiation with and without black ink on instrumented root canal walls, and the degree of both coronal and apical microleakage of filled root canals. Methodology Seventy-two single-rooted teeth were instrumented up to a size 40 K-file, and then divided into six groups of 10 teeth: groups 1 and 4 remained unlased and acted as control groups, groups 2 and 5 were treated with a Nd:YAG laser (Fidelis Plus, Herzele, Belgium), groups 3 and 6 were treated with a laser and black ink; the remaining 12 teeth served as positive and negative controls. The laser was operated at 1.5 W, 15 Hz, four times for 5 s with a 20-s interval. Groups 4-6 were filled using cold lateral condensation of gutta-percha and AH26. After storage in water for 48 h at 37 degrees C, through-and-through leakage (L in mu L day(-1)) was measured for 48 h under a pressure of 1.2 atm using a fluid transport model and recorded as L = 0 (L1), 0 < L <= 10 (L2), L > 10 (L3). After the assessment of leakage with the fluid transport model, the teeth were immersed in rhodamine B solution for 48 h at 37 degrees C. Apical and coronal dye leakage was scored after longitudinal splitting of these teeth. All teeth of groups 1-3 were split longitudinally and observed under SEM for evaluation of remaining smear layer. Results Through-and-through leakage was only observed in the group lased with black ink (two samples - L2). Apical and coronal dye leakage was observed in all groups; there were no statistically significant differences amongst the three experimental groups. The through-and-through leakage, measured with the fluid transport model in two teeth of group 6, was confirmed in the dye leakage test (rhodamine B dye was observed along the total length of the root filling). There was evidence of melted and ablated root canal dentine in the laser-treated groups. These findings were more obvious in root canals lased in association with black ink. All apical foramina in the lased group remained patent. Conclusions Nd:YAG laser irradiation with black ink increased the amount of melted and ablated dentine areas compared with that without black ink. Nd:YAG lasing in association with black ink did not result in a reduction of either coronal or apical microleakage in root filled teeth.