The crystalline structure of the starch of six cultivars of rice for sake brewing were studied by small-/wide-angle X-ray scattering and X-ray diffraction by synchrotron radiation. The starch structures all provide a lamella structure of a crystal phase and an amorphous phase. The crystal phases of the starches show A-type starch and some B-type starch. The B-type starch content varied slightly between the different rice cultivars, with Yamadanishiki-type containing the most. The change in starch structure upon the early stage of sake brewing was also investigated. The crystal structure and lamella structure were maintained after soaking in water. However, the structure of starch changed to an amorphous phase upon steaming and gelatinization. While the steamed rice was cooled at 15 °C, the starch crystal structure, but not lamella structure, was recovered. Furthermore, the dependence of B-type starch content on the cultivars was also recovered. This result indicated that the crystals of starch destroyed imperfectly, but also crystalline nuclei remained after steaming.