This article describes the alignment accuracy of the x-ray stepper that was codeveloped by the SORTEC Corporation and Matsushita Electric Industrial Co., and installed in the Tsukuba Research Laboratory for the SORTEC Corporation [K. Koga et al., J. Vac. Sci. Technol. B 8, 1633 (1990)]. Although the optical heterodyne method used for the stepper has a high position detection sensitivity, this method has the drawback that the alignment accuracy is apt to be influenced by an uncontrollable interference, because it uses a coherent laser light source. The overlay accuracy of the stepper was evaluated and identified the error factor contributing to the total overlay error. It was found that the deterioration of the alignment accuracy resulting from position detection error is caused by subtle deflection in the optical alignment system. In order to solve this problem, the alignment unit of the x-ray stepper has been improved. As a result, an alignment accuracy of less than 24 nm (3sigma) was obtained in a double-exposure experiment with a posiresist. In addition, an alignment accuracy of less than 38 nm (3sigma) was also obtained with SiO2 etched marks.