The paper presents chemical and structural analysis of geopolymer materials which are obtained by alkali-activated calcined clay (metakaolin) originated from Serbia under strictly defined conditions. Characterization of the metakaolin and geopolymers molecular structure has been done using X-ray diffraction, scanning electron microscope, Fourier transform infrared spectroscopy and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The paper presents the possibility of obtaining geopolymer structure and differences in chemical and structural characterization of these materials taking into account the concentration of NaOH as a variable parameter. The results of MALDI analysis of metakaolin and synthesized geopolymer structures using various matrix system: 2,4,6 trihydroxyacetophenone (THAP), α-cyano-4-hydroxycinnamic, 2,6 dihydroxyacetophenone and laser desorption/ionization, have shown that THAP matrix is the most appropriate for analysing these aluminosilicate materials.