Clay-based nanostructures were prepared from kaolinites of varying structural order by two different methods. In the first method the kaolinite-urea precursor, obtained by dry grinding, was intercalated further with triethanolamine and the tetraalkylammonium salt was synthesized in the interlamellar space. Exfoliation was achieved by the use of sodium polyacrylate (PAS). In the second method, the kaolinite-potassium acetate (kaolinite-KAc) precursor, obtained via two different methods, was intercalated further with ethylene glycol (EG) and then n-hexylamine (HA). Intercalation with EG was also achieved by heating either directly or with microwaves. The morphology that results depends on the method of precursor preparation, the method of heat treatment and the degree of structural order of the original clay. Higher structural order facilitates the formation of a tubular morphology, while mechanical treatment and microwave agitation may result in broken tubes. Molecular mechanical (MM) calculations showed that organo-complexes may be exfoliated to a d value of 10–11 Å.