Kaolinite, dickite, and pyrophyllite in CSSJ reference clay samples were investigated by S/TEM imaging, X-ray microanalyses in SEM and STEM, as well as XRD analysis to characterize mineral impurities, grain sizes, crystal structures, and other properties. The new lot of Kampaku kaolinite (JCSS-1101c) is almost free of quartz and alunite, which were abundant in the previous lot (JCSS-1101b). Svanbergite (SrAl₃(PO₄)(SO₄)(OH)₆) was identified as a minor mineral impurity in both lots by STEM-EDS analysis. The peaks characteristic of ordered kaolinite (kaolinite-1A) in the 02, 11 band are distinct (Hinckley Index＝1.17) in the new lot compared to those in the previous lot. This difference is likely to correspond to the higher proportion of large, well-ordered grains in the new lot. Shokozan dickite (JCSS-1301) also contains svanbergite, along with quartz, diaspore, and pyrophyllite as mineral impurities. Regarding kaolin group mineral polymorphs, XRD analysis indicated significant amounts of nacrite and kaolinite in addition to dickite. S/TEM imaging suggested that this sample has a bimodal grain-size distribution. The smaller grains with lateral sizes of less than 0.1 µm, may represent a disordered kaolin phase. In contrast, the larger grains are well-ordered dickite or nacrite with a two-layer periodicity. Shokozan pyrophyllite (JCSS-2101) contains quartz and diaspore as mineral impurities. Heavy stacking disorder with two alternative interlayer displacements was identified by HRTEM, which accounts well for the profile of the 02, 11 band in the XRD pattern.