Acetylenic amine derivatives of the 5,8-quinolinedione were synthesized and characterized by the 1 H and 13 C NMR, IR spectroscopy and MS spectra. Additionally, the 6-and 7-substituted allylamine-5,8-quinolinediones were synthesized for comparison purposes. The crystal structure was determined for the 6-chloro-7-propargylamine-5,8-quinolinedione and 7-chloro-6-propargylamine-5,8-quinolinedione. Additionally, the IR spectral analysis supplemented by the density functional theory (DFT) calculations were carried out. It was found that different positions of the propargylamine side chain had a distinct influence on crystal structure, formation of H-bonds and the carbonyl stretching IR bands. Correlation between the frequency separation ∆ν of the carbonyl IR bands and the position of the 6-and 7-substituents was found. The 7-substituted derivatives exhibited a higher frequency separation ∆ν. The observed correlation could provide an opportunity to use the IR spectroscopy to study substitution reactions. Cytotoxic activities against three human cancer cell lines for the 5,8-quinolinedione derivatives with different amine substituents, i.e., propargylamine, N-methylpropargylamine, 1,1-dimethylpropargylamine, allylamine and propylamine were also analysed with respect to their molecular structure.