Modelling of experimental X-ray diffraction (XRD) patterns is used to determine the phase composition of partially dehydroxylated kaolinite samples. To identify unambiguously the presence of two or three phases in the heated kaolinite samples, the full range of their XRD patterns has to be analysed. Two different kaolinites, from Imerys (UK) and from Georgia (USA; KGa-21), were studied. The heating temperatures were selected to cover the entire range of dehydroxylation for both kaolinites (400–550°C for Imerys and 400–495°C for KGa-21). Two different dehydroxylation pathways were observed. At each stage of partial dehydroxylation, the kaolinite from Imerys consisted of the original, non-dehydroxylated kaolinite and of a fully dehydroxylated phase, metakaolinite. During partial dehydroxylation of kaolinite KGa-21, each product formed at a given heating temperature consisted of three phases: the original kaolinite; a dehydroxylated phase, metakaolinite; and a phase with diffraction features corresponding to a defective kaolinite-like structure. To determine the content of metakaolinite in a partially dehydroxylated specimen, its experimental XRD pattern was reproduced by the optimal summation of the diffraction patterns of the initial kaolinite and metakaolinite. A procedure that reveals the basic diffraction features of the third phase is suggested. The XRD patterns and thus the structures of the metakaolinites formed after dehydroxylation of the Imerys and KGa-21 samples differ substantially. The conventional determination of the initial kaolinite and metakaolinite contents in partially dehydroxylated kaolinite based on the analysis of basal reflections and weight losses may lead to overlooking the formation of the intermediate phases.