The aim of our study was to evaluate the potential of en face optical coherence tomography (OCT) for the detection of apical microleakage after 980 nm and 1,064 nm laser-assisted endodontic treatment. Ninety, human, single-rooted teeth with one straight root canal and closed apices were used. All roots were prepared biomechanically to the working length at an apical size 30 and 0.06 taper. The teeth were divided into three equal groups of 30 samples each, according to the treatment to be applied to the root canal. Group I received 980 nm diode laser (3 W, 0.01 s on time, 0.01 s off time, 5 s per procedure, four procedures); group II received neodymium:yttrium-aluminum-garnet (Nd:YAG) laser (1.5 W, 15 Hz, 5 s per procedure, four procedures). In group III the root canals were approached conventionally only. In all groups the root canal filling was performed with AH Plus endodontic sealer and gutta-percha points. An en face OCT prototype was used for the investigation of apical microleakage. According to one-way analysis of variance (ANOVA) and en face OCT, the number of defects in the laser groups was significantly lower (P < 0.005) than in the control group. No statistical differences were noted between the laser groups (P = 0.049). En face OCT imaging proved that laser-assisted endodontic treatment improved the prognosis of root canal filling and led to a reduction in apical microleakage.