An alignment apparatus for substrates comprises a first movement mechanism moving a substrate to be treated in a horizontal direction, a second movement mechanism moving the substrate in a vertical direction, a rotation mechanism rotating the substrate in a substrate plane, an illumination tool irradiating the substrate from a sidewise direction in a state where the substrate is held in a desired height position by the second movement mechanism, an image sensor picking up an image on a back surface of the substrate in an irradiated state, an edge position sensor sensing plural edge positions of the substrate from an image obtained by the image sensor, and a control computer obtaining a positional shift of the substrate based on the edge positions sensed by the edge position sensor and correcting a positional shift of the horizontal and rotation directions by the first movement and rotation mechanisms.