Radiolysis of water by ionizing radiation results in the production of pure hydroxyl radicals. This technique, combined with analysis by tandem mass spectrometry (MS/MS), has been used to study the effect of hydroxyl radicals on the intact bovine alpha-crystallin protein. After exposure to gamma-irradiation, the oxidized alpha-crystallin was digested with trypsin and the resulting peptides were fractionated by reverse-phase HPLC. The isolated fractions were analyzed by matrix-assisted laser desorption ionization and by MS/MS to determine the locations and identities of the modifications. Structural analysis revealed that methionine 1 of alpha A- and alpha B-crystallin and methionine 68 of alpha B-crystallin were oxidized to methionine sulfoxide. Hydroxytryptophan was formed from each tryptophan residue in alpha-crystallin, although only tryptophan 9 of alpha A-crystallin was converted into N-formylkynurenine. This study has, for the first time, identified the sites of modification and the structures produced in the intact alpha-crystallin protein by exposure to hydroxyl radicals. By determining the consequences of in vitro exposure of alpha-crystallin to pure hydroxyl radicals, the in vivo contribution of this reactive oxygen species to the overall oxidative stress of the lens will be achieved from the identification of the modifications to alpha-crystallin purified from intact human lenses.