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The cross grid encoder is an optical diffraction grating type encoder to measure two-dimensional position of a optical head by using a grid plate where grids are aligned orthogonal to each other. The cross grid encoder can be applied to measure two-dimensional motion errors of high-precision and ultra-precision machine tools, such as the straightness error or the squareness error. As a basis to establish a methodology to measure evaluate motion accuracy of high- and ultra-precision machine tools by using the cross grid encoder, this paper presents a self-calibration scheme of a measurement error of the cross grid encoder caused mainly by the misalignment of grids. The measurement error corresponding to the location on the grid plate is calibrated by comparing three measurements taken with different orientation of the grid plate. It is experimentally validated that the measurement error of the cross grid encoder is reduced by about 85% at maximum by applying the self-calibration and the compensation of measurement errors.