Peroxidase-catalyzed halogenation reactions have been established as being important in the biosynthesis of the hormone thyroxine and in biological defense mechanisms. Recently these reactions have been recognized as valuable tools for the study of proteins as well as their arrangement in macromolecular structures. The pathways of peroxidase catalyses can be accommodated within the framework of the classical Chance-George mechanism. This implies that the initial steps of the reaction invariably involve oxidation of peroxidases by peroxides--and that the resulting derivative, compound I, is the oxidant of the halide ions. Such reactions may result either in the formation of hypohalous acids, or in halogenation of the enzyme apoprotein, followed by transhalogenation to substrate for halogenation. Chloro- and myeloperoxidases catalyze oxidation of all halide ions, except F-; oxidation of bromide and iodide is mediated by lactoperoxidase, but horseradish peroxidase only oxidizes iodide. All of the above enzymes except horseradish will oxidize the pseudo halide thiocyanate. The origins of this differentiation remain to be defined, but they presumably reflect significant variation in oxidation potential of different peroxidase-peroxide derivatives, rather than constraints on the peroxidase-donor interactions. As pointed out above, halogenation of the amino acids tyrosine and histidine or these residues in proteins can take place on the enzyme. This makes lactoperoxidase-catalyzed iodination selective. The amino acid residues in proteins that are iodinated depend not only on reactivity of the amino acid residue but also on its geometric location. Thus lactoperoxidase-catalyzed iodination can be a useful tool in the study of protein structure and function. It is also useful in establishing the geometric position of proteins within macromolecular structures. Thyroid peroxidase catalyzes iodination of thyroglobulin and is involved in a second important step, the coupling of the iodotyrosines to form thyroxine or triiodothyronine. A proposed mechanism for this reaction suggests that the oxidation is mediated by the iodoenzyme derivative mentioned above followed by a prototropic rearrangement and scission to form the ether bound of thyronine and a serine residue on thyroglobulin.