The protonation process of citraconic and glutaconic acid in perchloric acid media was followed using the method of UV spectroscopy. The observed changes in the UV spectra of investigated acids confirmed that the protonation process in perchloric acid with concentration from 5 to 10 mol/dm3 occurred. Glutaconic acid behaved as weak organic base in perchloric acid media and existed in its monoprotonated form. On the other hand, citraconic acid existed in its protonated form and as protonated anhydride at higher perchloric acid concentration. Using the absorbance data the thermodynamic dissociation constants were calculated applying the methods of Yates and McClelland, Bunnett and Olsen, and the “excess acidity” function method. The solvatation parameters m, m* and f were evaluated, as well. In order to correct the medium effect the method of characteristic vector analysis was applied. The possible site where the protonation may take place was discussed using the partial atomic charge values determined according to AM1 and PM3 semiempirical methods.