The utilization of new transmission X-ray microscopy (TXM) using the synchrotron photon source enable for the first time the study in three dimensions microsize clay particles in aggregates in their natural aqueous environment. This technique makes possible remarkable accurate images of nanosize mineral interparticle structure which forms a new nanocomposite. The Birdwood kaolinite/LDH aggregates observed in the TXM are much more compact than observed before in pure Birdwood kaolinite suspension and similar to aggregates formed after treatment by positively charged surfactant. Kaolinite/LDH aggregates in water reveal complex structure of larger kaolinite platelets connected together by gelled nanoparticles which are most probably LDH colloidal plates. Comparisons of the transmission electron microscope (TEM) and TXM techniques show similarities in particle morphology. The ability to study particles and aggregates in their natural aqueous environment and in 3-dimensions make this technique superior to the TEM technique.