Single and double proton-transfer reactions in Watson-Crick Guanine- Cytosine (GC) and Adenine-Thymine (AT) radical cations have been studied using the hybrid density functional B3LYP method. Calibration calculations for the formamidine-formamide dimer, a model system of AT, have shown that B3LYP compares well to the high level ab initio correlated method CCSD(T), both for the neutral and cationic systems. The single proton-transfer reaction is favorable in both the GC and AT radical cations; it takes place from the ionized monomer (guanine and adenine, respectively), which increases its acidity, to the neutral fragment. For the two systems, GC and AT, the nonproton transferred and single proton transferred structures are almost degenerate (ΔE = 1.2 kcal/mol), and the process presents low energy barriers (4.3 kcal/mol for GC and 1.6 kcal/mol for AT). The double proton-transfer reaction is less favorable than the single one, in contrast to what is observed for the neutral systems. The relative stability of the different structures can be understood considering two factors: the relative stability of the asymptotes from which they derive and the number and sequence of the strong and weak hydrogen bonds formed. For the same number of strong short hydrogen bonds, the most stable structures are those in which the strong H- bonds are neighbors. Based on these considerations, a prediction for other pairings is reported.