Differentiating clay minerals that formed in a supergene environment during deep chemical weathering from those that formed during hydrothermal alteration at higher temperatures associated with a mineralizing event is important in the exploration for epithermal Au deposits. The purpose of this study was to further elucidate this topic by comparing morphological and chemical properties of clay minerals in saprolite overlying epithermally altered bedrock at the Vera Au deposit, Queensland, Australia, with those of clay minerals in saprolite overlying bedrock adjacent to the epithermal alteration zone. X-ray diffraction (XRD) and analytical transmission electron microscopy (ATEM) investigations identified kaolinite, illite, and interstratified illite-smectite, together with quartz, Fe and Ti oxide minerals, and the sulfate minerals jarosite, gypsum, alunite, and natroalunite. Kaolinite crystals within the weathered argillic alteration zone proximal to the epithermal quartz vein are generally larger (up to 3 μm in diameter) and better formed (subhedral to euhedral) than crystals in saprolite distal to the hydrothermal alteration zone, in which smaller (mostly <1 μm), subhedral to anhedral crystals dominate. Energy-dispersive spectrometry (EDS) analysis of single crystals indicated that kaolinite within the alteration zone has an Al/Si ratio indistinguishable from reference kaolinite and has small Fe concentrations, whereas distal saprolitic kaolinite has smaller Al/Si and greater Fe/Si ratios, consistent with the formation of low-Fe kaolinite during hydrothermal alteration and higher-Fe kaolinite during weathering. Illite and interstratified illite-smectite (I-S) were distinguished from kaolinite by their morphology and greater K/Si and smaller Al/Si ratios. The Illite and I-S morphology ranged from thin irregular masses through lath-like crystals in hydrothermal samples to larger, irregularly shaped crystals. The Ca/Si and K/Si ratios of single crystals in Ca-saturated clay minerals were consistent with the I-S interstratification parameters determined from XRD patterns.