Remineralization is the process by which hydroxyapatite (HAp) is restored in enamel subsurface lesions, and transversal microradiography (TMR) has been used to analyze remineralization in terms of the recovery of mineral content. In this study, we directly detected the distribution and orientation of longitudinal HAp crystallite at the remineralized zone in enamel subsurface lesions by using an X-ray microbeam (6-µm diameter) diffraction method. This method was demonstrated and involves the simultaneous detection of wide-angle X-ray diffraction (WAXRD) and small-angle X-ray scattering (SAXS). WAXRD reflects the amount of HAp crystallites, and SAXS reflects that of voids in crystallites. The polished surface of a bovine enamel block was divided into three zones of sound, demineralized, and remineralized zones. Thin sections of approximately 150 µm thickness were then cut perpendicular to the surface, and subjected to WAXRD and SAXS following TMR. The increase in the amount of HAp crystallites and the decrease in voids in the crystallites at the remineralized zone were detected by WAXRD and SAXS, respectively, which was consistent with the result of TMR. This study indicates that both the spatial distribution and orientation of the restored HAp crystals in the remineralization process at the subsurface lesion can be simultaneously analyzed by the X-ray diffraction methods.