SAXS and EXAFS were applied to study genesis of polynuclear zirconium hydroxyspecies in pillaring solutions as dependent upon the zirconium concentration, addition of alkaline-earth chlorides and aging. After the montmorillonite clay pillaring, the structure of zirconium nanopillars was characterized by applying X-ray structural analysis, UV-Vis, FTIRS of adsorbed CO and nitrogen adsorption isotherms. Main pillaring species appear to be nanorods comprised of several Zr4 tetramers. Basic structural features of the tetramers are preserved in zirconia nanoparticles fixed between alumosilicate layers in pillared clays. In calcined samples, those nanoparticles contain only bridging hydroxyls and/or oxygen anions responsible for bonding within pillars and between pillars and clay sheets.