The reaction of purified bovine mitochondrial cytochrome c oxidase (CcO) and hydrogen peroxide was studied using the ESR spin-trapping technique. A protein-centered radical adduct was trapped by 5, 5-dimethyl-1-pyrroline N-oxide and was assigned to a thiyl radical adduct based on its hyperfine coupling constants of aN = 14.7 G and abetaH = 15.7 G. The ESR spectra obtained using the nitroso spin traps 3,5-dibromo-4-nitrosobenzenesulfonic acid (DBNBS) and 2-methyl-2-nitrosopropane (MNP) indicated that both DBNBS/.CcO and MNP/.CcO radical adducts are immobilized nitroxides formed by the trapping of protein-derived radicals. Alkylation of the free thiols on the enzyme with N-ethylmaleimide (NEM) prevented 5, 5-dimethyl-1-pyrroline N-oxide adduct formation and changed the spectra of the MNP and DBNBS radical adducts. Nonspecific protease treatment of MNP-d9/.NEM-CcO converted its spectrum from that of an immobilized nitroxide to an isotropic three-line spectrum characteristic of rapid molecular motion. Super-hyperfine couplings were detected in this spectrum and assigned to the MNP/.tyrosyl adduct(s). The inhibition of either CcO or NEM-CcO with potassium cyanide prevented detectable MNP adduct formation, indicating heme involvement in the reaction. The results indicate that one or more cysteine residues are the preferred reductant of the presumed ferryl porphyrin cation radical residue intermediate. When the cysteine residues are blocked with NEM, one or more tyrosine residues become the preferred reductant, forming the tyrosyl radical.