The effect of protonation on the electron density of a series of small molecules has been studied by means of the quantum theory of the Atoms in Molecules (QTAIM) methodology. The nonuniform redistribution of the electron density upon protonation of the systems produces an increase of the atomic energy of the protonated heteroatom and a reduction of the atomic charge for the protonated oxygen, while an increase of the charge on the protonated nitrogens is observed. The total volume of the protonated systems is smaller than that of the corresponding neutral ones. Thus, all the groups that form the molecule suffer a reduction of the volume when the systems become protonated. The transferability of the methyl group properties between the molecules studied has been analyzed.