This review demonstrates that high-resolution transmission electron microscopy (HRTEM) imaging of clay minerals or phyllosilicates with an incident electron beam along the major zone axes parallel to the constituting layers, in which the contrast corresponds to individual cation columns in the images obtained, is indispensable for elucidating the enigmatic structures of these minerals. Several kinds of variables for layer stacking, including polytypes, stacking disorder and the interstratification of various kinds of unit layers or interlayer materials, are common in phyllosilicates. Local and rigorous determination of such variables is possible only with HRTEM, although examination as to whether the results obtained by the HRTEM images from limited areas represent the whole specimen should be made using other techniques, such as X-ray diffraction. Analysis of these stacking features in clay minerals provides valuable insights into their origin and/or formation processes. Recent state-of-the-art techniques in electron microscopy, including incoherent imaging, superior resolutions of ~0.1 nm and low-dose imaging using new recording media, will also contribute significantly to our understanding of the true structures of clay minerals.