Two examples of phase transition in self-assembled mesostructured hybrid thin films are reported. The materials have been synthesized using tetraethoxysilane as the silica source hydrolyzed with or without the addition of methyltriethoxysilane. The combined use of transmission electron microscopy, small-angle X-ray scattering and computer simulation has been introduced to achieve a clear identification of the organized phases. A structural study of the self-assembled mesophases as a function of thermal treatment has allowed the overall phase transition to be followed. The initial symmetries of mesophases in as-deposited films have been linked to those observed in samples after thermal treatment. The monodimensional shrinkage of silica films during calcination has induced a phase transition from face-centered orthorhombic to body-centered cubic. In hybrid films, instead, the phase transition has not involved a change in the unit cell but a contraction of the cell parameter normal to the substrate.