The reduction of methionine sulfoxide with ammonium iodide in trifluoroacetic acid has been studied in peptides containing cysteine, histidine, tyrosine or tryptophan residues. While histidine and tyrosine have proved to be stable under the experimental conditions, cysteine is oxidized to cystine and tryptophan dimerizes to form 2-indolylindolenine derivatives. The use of methyl sulfide to increase the reduction rate minimizes the problem and protection of indole ring with the formyl group avoids the side reaction for this amino acid. (C) 1998 Elsevier Science Ltd. All rights reserved.