We present a new three-step auto-alignment algorithm for the specimen stage of an ellipsometer with adjustable angle of incidence. Correction of errors in tilt angle and position of the specimen stage can be performed by locating the reflected light spot at the center of the detector at two different angles of incidence. The current method does not need auxiliary focusing equipment. The alignment algorithm works to high precision in both model simulation and practical experiments with a rotating analyzer ellipsometer. (C) 2002 American Institute of Physics.