The change of crystalline structure in hydrothermally treated hinoki wood was investigated by means of Fourier-transform near-infrared spectroscopy in combination with a deuterium exchange method and X-ray diffraction. The results were compared with analogous data of dry-exposed archeological wood taken from an old wooden temple. Although the decomposition of the amorphous regions in cellulose and hemicelluloses, which corresponds to an increase of the degree of crystallinity, was observed for both, archeologically and hydrothermally treated wood, the increase of crystallite thickness was confirmed only for hydrothermally treated wood. The increase of the average size of crystallites corresponds well to the measured decrease of the deuteration accessibility of the crystalline regions. As the accessibility of the crystalline regions decreased for both, D2O and t-butanol, it is assumed that due to the expansion of the crystalline domains by hydrothermal treatment several elementary fibrils are arranged at distances below 0.3 nm.