To evaluate the types of amino acid thermal transformations caused by silicate materials, we studied the volatilization products of Aib, L-Ala, L-Val and L-Leu under temperatures of up to 270 °C in the presence of silica gel as a model catalyst and pulverized basaltic lava samples. It was found that silica gel catalyzes nearly quantitative condensation of amino acids, where piperazinediones are the major products, whereas lava samples have much lower catalytic efficiency. In addition bicyclic and tricyclic amidines and several products of their subsequent thermal decomposition have been identified using the coupled technique of GC-FTIR-MS and HPLC-PB-MS, with auxiliary computer simulation of IR spectra and NMR spectroscopy. The decomposition is due to dehydrogenation, elimination of the alkyl substituents and dehydration as well as cleavage of the bicyclic ring system. The imidazole ring appears to be more resistant to thermal decomposition as compared to the pyperazine moiety, giving rise to the formation of different substituted imidazolones. The amidines were found to hydrolyze under treatment with concentrated HCl, releasing the starting amino acids and thus behaving as amino acid anhydrides. The thermal transformations cause significant racemization of amino acid residues. Based on our observations, the formation of amidine-type products is suggested to be rather common in the high-temperature experiments on amino acid condensation.