Sol−gel polymerization of organotrialkoxysilanes RSi(OR‘)₃ and formation of silsesquioxane (SSQO) structures was followed using SEC, ²⁹Si NMR, and both small- and wide-angle X-ray scattering. Evolution of the SSQO structure is controlled by the competition between intermolecular polycondensation and cyclization. A strong tendency to buildup of polyhedral cyclic oligomersmainly octamer “cages” and larger cagelike structureswas found to grow with increasing size of substituent R. As a result, long substituents prevent gelation of the trifunctional system and increase stability of the SSQO. Because of incompatibility of the polyhedral SSQO framework and pendant organic chains, microphase separation takes place and spontaneous self-organization occurs. A micellar arrangement of compact SSQO domains with a correlation distance corresponding to the size of the substituent is formed, and the ordering is promoted by increasing length of the organic chain. The most organized arrangement was observed with the trialkoxysilanes substituted with long PEO chains which crystallize and force the SSQO cages to align in the lamellar structure.