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Kaolins and clays are important raw materials for production of supplementary cementitious materials and geopolymer precursors through thermal activation by calcination beyond dehydroxylation (DHX). Both types of clay contain different polytypes and disordered structures of kaolinite but little is known about the impact of the layer stacking of dioctahedral 1:1 layer silicates on optimum thermal activation conditions and following reactivity with alkaline solutions. The objective of the present study was to improve understanding of the impact of layer stacking in dioctahedral 1:1 layer silicates on the thermal activation by investigating the atomic structure after dehydroxylation. Heating experiments by simultaneous thermal analysis (STA) followed by characterization of the dehydroxylated materials by nuclear magnetic resonance spectroscopy (NMR) and scanning electron microscopy (SEM) together with first-principles calculations were performed. Density functional theory (DFT) was utilized for correlation of geometry-optimized structures to thermodynamic stability. The resulting volumes of unit cells were compared with data from dilatometry studies. The local structure changes were correlated with experimental results of increasing DHX temperature in the following order: disordered kaolinite, kaolinite, and dickite, whereupon dickite showed two dehydroxylation steps. Intermediate structures were found that were thermodynamically stable and partially dehydroxylated to a degree of DHX of 75% for kaolinite, 25% for disordered kaolinite, and 50% for dickite. These thermodynamically stable, partially dehydroxylated intermediates contained AlV while metakaolinite and metadickite contained only AlIV with a strongly distorted coordination shell. These results indicate strongly the necessity for characterization of the structure of dioctahedral 1:1 layer silicates in kaolins and clays as a key parameter to predict optimized calcination conditions and resulting reactivity.