In a substrate alignment apparatus, a motor sequentially rotates a plurality of substrates in a circumferential direction, the substrates being to be held in a vertical posture at a lower edge portion by a substrate holder. A controller controls the motor on the basis of warpage-and-notch-position information and input information that is input about a warped state of the substrates, to determine circumferential positions of the notches of the substrates. This reduces a distance in a thickness direction between a lower edge portion and an upper edge of each substrate that is held by the substrate holder. As a result, it is possible to facilitate handling of a plurality of substrates held by the substrate holder.