As the hydroxyl (OH) and perhydroxyl (OOH) radicals are known to play important roles in biological systems, their reactions with cytosine and thymine were studied. Addition reactions of these radicals at different sites of cytosine and thymine, and hydrogen abstraction reactions by each of the two radicals from the different sites of the two molecules were studied at the B3LYP/6-31G(d,p), B3LYP/AUG-cc-pVDZ and BHandHLYP/AUG-cc-pVDZ levels of density functional theory. Effect of solvation in aqueous media on the reactions was studied at all these levels of theory using single point energy calculations using the polarizable continuum model. The present study shows that whereas the OH radical would abstract H atoms from the various sites of cytosine and thymine efficiently, the OOH radical would have poor reactivity in this regard. The OH radical is also predicted to be much more reactive than the OOH radical with regard to addition reactions at the C5 and C6 sites of both thymine and cytosine, though the OOH radical is also predicted to have significant reactivity in this respect. © 2012 Wiley Periodicals, Inc.