A grazing incidence ultra-small-angle X-ray scattering measurement system using a laboratory X-ray source has been developed. Submicron-scale artificial periodic grooves on thermally oxidized silicon wafers are characterized using this system. They are fabricated by electron beam lithography. The average pitch widths of the grooves are determined accurately with a low standard uncertainty of less than 0.02%. The cross-sectional profiles are also analyzed by intensity ratios of higher-order diffraction peaks from the periodic structures and X-ray reflectivity measurements. The obtained cross-sectional profiles are in good agreement with those obtained by atomic force microscopy.