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Structure and thermal behavior of organoclays has an important influence on properties of clay-based polymer nanocomposites. Depending on starting mineral and amphiphilic compounds, various organoclays were produced. A synthetic silicate was modified with stoichiometric amounts of 3 various quaternary alkylammonium salts and studied by calorimetry and SAXS. The interlayer spacing of silicate, calculated from the main diffraction maximum, grows strictly linearly with the length of long aliphatic chains bonded to quaternary nitrogen atoms. Further analysis of the diffractograms leads to the conclusion that the ion exchange results in formation of a mixture of 3 phases with different values of interlayer spacing. Quaternary ammonium cations may undergo phase transitions similar to the moieties in the bulk. The temperature range of the transitions was however found to be distinctly shifted towards lower values in comparison to the alkylammonium salts alone. Thermogravimetric analysis was used to estimate thermal stability and the coverage of silicate surface with amphiphilic molecules.