This article aimed to separate and identify molecular species obtained in the sol-gel process by gas chromatography coupled with mass spectrometry (GC-MS), for the reaction mixture with methyltrimethoxysilane (MTMOS). In the presence of an unhydrolyzed methyl group, the molecular species starting with the cyclic trimers, a series of geometric isomers were separated and identified due to the position of the methyl groups in relation to the ring plane of each siloxane molecule; in addition, for the hydrolyzed products, isomers with different relative positions of the hydroxyl groups to the methyl and methoxy groups were separated and identified. The reactivity of the new molecular species formed determines subsequent stages of the sol-gel process.