Near-atomic resolution TEM imaging has been successfully applied to determine the stacking defect structures in kaolin minerals, especially kaolinite. The specimen studied is from the middle stage of the depth-related kaolinite-to-dickite transformation in a sandstone reservoir. Several high-quality images were recorded on films in which the tetrahedral and octahedral positions in the kaolinite unit layers are clearly resolved, despite the obstacle of electron radiation damage. Electron diffraction and high-resolution imaging of dickite showed that few stacking defects exist in this polytype. On the other hand, kaolinite crystals contain a high density of stacking defects. These defects or stacking disorders are formed by a mixture of two kinds of lateral interlayer shifts, t1 (approximately −a/3) and t2 (−a/3 + b/3), between adjacent layers. Disorder due to the coexistence of B and C layers (dickite-like stacking sequence) was never observed. These results provide not only an unambiguous settlement for the long -standing controversy of the defect structures in kaolinite, but also a new clue to understanding the kaolinite-to-dickite transformation mechanism.