An auto focus system includes a stage on which a substrate is mounted, light sources that irradiate the substrate with a plurality of focus beams directed towards the substrate at different angles, sensors that detect the focus beams reflected from the substrate, and a controller that determines the relative location of a surface of the substrate according to the locations at which the focus beams are detected by the sensors and positions the substrate accordingly. To this end, the controller performs calculations that are free from the influence of variations in the refractive index of the medium through which the focus beams propagate to the surface of the substrate. Therefore, the autofocus process is carried out with a high degree of precision.