The results of an ab initio post-Hartree-Fock study of the protonation of all nucleic acid bases are reported. Rare tautomers of guanine and cytosine, which coexist in the gas phase with the major forms, were also included in the study. The geometries of the local minima and transition states were optimized without symmetry restrictions by the gradient procedure at the HF and MP2 levels of theory and were verified by energy second-derivative calculations. The standard 6-31+G(d,p) basis set was used. The single-point calculations have been performed at the MP4(SDTQ)/6-31 +G(d;p)//MP2/6-31 +G(d,p) and MP2/6-311 ++G(d,p)//MP2/6-31 +G(d,p) approximations. The relative stabilities of the different protonated forms of all nucleic acid bases have been reported. The values of proton affinities (PA) for each base including contributions of rare tautomers and different protonated forms for guanine and cytosine have been calculated. We have shown that the calculated values of proton affinities are very close to the experimental data, and the differences are in the range of 0.0-2.1%. We have concluded that all levels of the Moller-Plesset theory considered in the study are able to describe the PA values of nucleic acid bases with experimental accuracy. The study has shown that the rare tautomers make up a significant portion of the gas-phase equilibrium mixture. Yet, the values of the proton affinities change only slightly with the inclusion of rare forms into the calculations.