The aims of this study were to obtain accurate structural information on the dimethyl sulfoxide (DMSO) and dimethylselenoxide (DMSeO) kaolinite intercalates, paying close attention to the hydrogen-bond geometries, and to provide a detailed interpretation of the individual vibrational modes of intercalates under study and relate their energies to the formation of the hydrogen bonds. Accurate positions of all the atoms in the structures of kaolinite:dimethylsulfoxide (K:DMSO) and kaolinite:dimethylselenoxide (K:DMSeO) intercalates have been obtained by the total energy minimization in solid state at density functional theory (DFT) level of the theory. The bond distances and angles in the kaolinite 1:1 layer are in good agreement with those reported in the most recent single-crystal refinement of kaolinite. Computed geometries of DMSO and DMSeO agree well with the high-quality diffraction data and independent theoretical ab initio calculations. The organic molecules are fixed in the interlayer space mainly by three moderately strong O–H…O hydrogen bonds, of different strengths, with the O…O contact distances being within 2.739–2.932 Å (K:DMSO) and 2.681–2.849 Å (K:DMSeO). Substantially weaker C–H…O and O–H…S(Se) contacts play only a supporting role. The optimized atomic coordinates were used to calculate the individual vibrational modes between 0 and 4000 cm−1. The maximum red shifts of the OH-stretching modes caused by the formation of the O–H…O hydrogen bonds were 407 cm−1 (K–DMSO) and 537 cm−1 (K-DMeSO), respectively. The Al–O–H bending modes are spread over the large interval of 100–1200 cm−1, but the dominant contributions are concentrated between 800 and 1200 cm−1. Theoretically calculated energies of the OH- and CH-stretching modes show good agreement with the previously published figures obtained from the infrared and Raman spectra of these intercalates.