Studies were carried out to develop a chromatographic methodology based on hydrophilic interaction liquid chromatography (HILIC) for the separation of various reaction products of hexamethylenetetramine (HMTA) –urea used in the sol–gel process for the preparation of ceramic microspheres. Different chromatographic parameters such as organic modifiers, pH of mobile phase, buffer concentration, column temperature, etc. were studied to arrive at the optimum conditions for separation. Compounds such as urea, monomethylolurea (MMU), dimethylolurea (DMU), and HMTA were separated from a synthetic mixture using a mobile phase consisting of acetonitrile and acetate buffer of pH 6. The methodology developed based on HILIC stationary phase is simple and amicable for integration with electrospray ionization mass spectrometry (ESI-MS) to identify the unknown reaction products. The methodology was applied for the separation of reaction products in pre-boiled and untreated urea–HMTA mixtures used as feed in the sol–gel process.