Kaolinite-smectite mixed-layers have been found to have a complex structure with smectite and kaolinite domains within layers. Here we further investigate this structure in samples with 0–80% kaolinite layers, as determined by X-ray diffraction, by means of magic angle spinning nuclear magnetic resonance (MAS NMR) of 29Si and 6Li. The 29Si NMR experiments were carried out on two samples (55 and 80% kaolinite layers), before and after their exchange with Mn2+, a paramagnetic ion that causes NMR signal loss from neighbouring nuclei, in order to investigate the distance between Mn ions and Si atoms in kaolinite sites. The 29Si NMR intensity from such sites (at ~−91 ppm) was reduced upon Mn exchange, indicating that some Mn ions are located near kaolinite Si sites. The position of the 6Li peak changes slightly (−1.3 to −1.8 ppm) but progressively with increasing kaolinite content (0–80% kaolinite layers) of four K-S specimens, suggesting two slightly different chemical environments for interlayer Li, one related to smectite and the other to kaolinite. The two sets of experiments are consistent with a complex structure of kaolinite-smectite, including smectite and kaolinite domains within layers and/or interlayers of varying smectitic and kaolinitic character.