We sought to evaluate the effects of Er:YAG laser (LightTouch, LightInstruments, Israel) conditioning on enamel roughness and shear bond strength of orthodontic brackets on enamel. Eighteen human molars (n = 9) and premolars (n = 9), were divided into 3 groups depending on the enamel conditioning method; Er:YAG laser (G1, n = 6), conventional etching with 37% orthophosphoric acid (G2, n = 6), Er:YAG laser combined with conventional etching (G3, n = 6). Er:YAG laser parameters were as follows: energy: 100 mJ, frequency: 10 Hz, exposure time: 10 s, applicator diameter: 600 μm, fluence: 35.37 J/cm2, distance: 1 mm away from a tooth, cooling: 80%. An MTS 858 MiniBionix® machine was used to determine the shear bond strength (MTS System, Eden Prairie, MN, USA). The enamel structure was assessed using X-ray microtomography (SkyScan 1172, Bruker, Kontich, Belgium). The highest values of shear bond strength were obtained in the G3 group (9.23 ± 2.38 MPa) and the lowest values in the G2 group (6.44 ± 2.11 MPa) (p < 0.05). A significant change in the enamel surface was noted after applying laser, reaching up to 9% of enamel thickness, which was not observed in the etched samples. Moreover, the Er:YAG laser-irradiated enamel surface was characterized by the greatest roughness. The combined use of an Er:YAG laser with a conventional etching improves the adhesion of composite materials to the tooth.