B3LYP and MP2 methods are used to study the hydroxylation and dehydrogenation of thymine at different sites in the presence of hydroxyl radicals (⋅OH). With a 6-311++G(d,p) level of description, the consistent results thermodynamically show that the relative free energy increases in the order of CM5 < N1 < C6 < N3 on the hydrogen abstraction. However, toward the hydroxylation, though the two methods give a similar trend that free energy barrier increases in the order of C6 < C5 < C4 < C2, they describe the reaction at C6 site in a different way: B3LYP calculation gives a barrierless pathway, whereas MP2 calculation gives a reactant complex with an energy of 19.5 kJ/mol and a pathway with a barrier energy of 64.9 kJ/mol. The calculated results are consistent with experimental data and the preference for the C5 site is due to the facility of ⋅OH in approaching the substrate. © 2013 Wiley Periodicals, Inc.