Provided is a position specifying system including: a light irradiation section that irradiates light to different positions of a physical body respectively; an image capturing section that captures images of an object existing inside the physical body, by means of the light irradiated to the different positions; and a position specifying section that specifies a depth of the object from a surface of the physical body onto which the light from the light irradiation section is irradiated, based on a difference in the images captured by the image capturing section.