1. An X-ray examination region setting method of setting an examination region for examining a substrate using X-rays, the method comprising the steps of: displaying a visible light image obtained by photographing the substrate from a perpendicular direction with respect to a substrate surface; accepting input of information for specifying a range within which a component mounted on the substrate is present in the displayed image; generating three-dimensional reconstruction data from an X-ray fluorography image obtained by performing X-ray fluorography on a three-dimensional region including a region of the component within the specified range; determining information on a position of a wiring connecting the substrate and the component by processing the three-dimensional reconstruction data; and determining, from the determined information on the position of the wiring, a region corresponding to the wiring within the three-dimensional region, and setting the determined region as the examination region; in the step of determining the information on the position of the wiring, data of a predetermined range in the perpendicular direction in the three-dimensional reconstruction data is taken as processing target, the predetermined range includes a position in the perpendicular direction where an accumulated value of luminance has a peak, the accumulated value of luminance being calculated at each position in the perpendicular direction from data obtained by overlapping, in a tomographic depth direction, pixels of a plurality of cross-sectional images parallel to each other and to the perpendicular direction of the three-dimensional reconstruction data.