The aim of this study is to assess the apical microleakage of the composite filled root-end cavities prepared by an Erbium, Chromium: Yttrium-Scandium-Gallium-Garnet laser. Fifty-five maxillary incisor teeth were enlarged and filled. Following the apical resection, root-end cavities were prepared using conventional methods: either using a bur (n = 30) or an ultrasonic retrotip (n = 15). Root-end cavities of the 15 teeth in the bur group were finished with the laser at 3.5 W. All root-end cavities were filled using two-step self-etching primer and composite resin. After 4 months of storage, apical microleakage was measured by a fluid filtration method. Microleakage of composite filled root-end cavities that were prepared by Er, Cr: YSGG was significantly larger than those made by conventional methods (p < 0.05). In conclusion, using the Er, Cr: YSGG laser has no advantages over conventional root-end cavity preparation methods when a composite filling material is used to seal root-end cavities.