The influence of the structure of potential medicines, i.e. methyl [4-oxo-8-(R-phenyl)-2,3,4,6,7,8-hexahydroimidazo[2,1-c][1,2,4]triazin-3-yl]acetates, on their melting points, thermal properties and decomposition paths has been assessed in inert and oxidizing conditions by the use of DSC and simultaneous TG/DTG/FTIR/QMS analyses. The melting points of particular molecules were directly dependent on their structure, and decreased as follows: the meta-Cl-substituted compound > the para-Cl-substituted compound > the parent compound (an unsubstituted structure) > the para-OCH3-substituted compound. The high thermal stability (above 240 °C) of the tested compounds in both furnace atmospheres was proved. The thermal resistance of these compounds increased in inert conditions as follows: the parent compound < meta- and para-Cl-substituted compounds < the para-OCH3-substituted compound, and decreased in oxidizing conditions as follows: the meta-Cl-substituted compound > the para-Cl-substituted compound > the para-OCH3-substituted compound > the unsubstituted compound. The pyrolysis process of the tested molecules resulted in the emission of CH3OH, NH3, HCN, HNCO, HCONH2, CH3CHO, aliphatic amines, alkenes, CH3Cl (for Cl-substituted compounds), CH4 (for the unsubstituted compound), aromatic compounds, CO2, CO and H2O. The oxidative decomposition process was connected with the formation of the same volatiles as during pyrolysis and additionally CH3COOH, CH3NO, NO and NO2. These studies confirmed that the pyrolysis and oxidative decomposition processes of hydrogenated heterofused as-triazines with an ester functional group at the C3 proceeded by the radical mechanism in both furnace atmospheres employed.