This work presents an overview of the data obtained for SBA-15 synthesis under the reaction conditions using synchrotron based small angle X-ray scattering and small angle neutron scattering. Three major stages in the synthesis of SBA-15 materials proceeding according to the cooperative self-assembly mechanism have been identified, and the structures of the intermediates species have been established. Our in situ time-resolved neutron scattering experiments demonstrate that only spherical micelles of the templating agent are present in the synthesis mixture during the first stage of the reaction. According to the neutron scattering and X-ray scattering data, in the second stage of the reaction the formation of hybrid organic–inorganic micelles is accompanied with the transformation from spherical to cylindrical micelles, which takes place before the precipitation of the ordered SBA-15 phase. During the third stage, these micelles aggregate into a two-dimensional hexagonal structure, confirming that the precipitation takes place as the result of self-assembly of the hybrid cylindrical micelles. As the synthesis proceeds, the voids between the cylinders are filled with the silicate species which undergo condensation reactions resulting in cross-linking and covalent bonding, leading to the formation of highly ordered SBA-15 mesostructure. This work demonstrates that valuable structural information can be obtained from X-ray and neutron scattering characterisation of complex systems containing periodic phases with d-spacing values up to 30 nm, and that both techniques are powerful means for in situ monitoring of the formation of nanostructured materials.