The applicability of resonance theory to explain the protonation of pyrimidinic bases was analyzed within the framework of the atoms in molecules (AIM) theory using B3LYP/6-31++G**//B3LYP/6-31G** charge densities of the neutral and diverse protonated forms of uracil and cytosine. The present study demonstrates that AIM atomic properties and delocalization indexes do not follow the trends that should be expected according to the resonance model. The resonance model is only able to predict the stability sequence of protonated forms and explain the changes exhibited by most of the bond properties upon protonations. Both the O- and N-protonated forms are found to be better described by RO-H+ and RN-H+ forms than by the classical RO+-H and RN+-H structures. According to the AIM analysis the electron charge gained by the proton is mainly provided by the other hydrogens of the molecule.