N(α)-Acetylation is the most frequently occurring chemical modification of the α-NH2 group of eukaryotic proteins and was believed until now to be catalyzed by a single N(α)-acetyltransferase. The transfer of an acetyl group from acetyl coenzyme A to the α-amino group of five NH2-terminal residues (serine, alanine, methionine, glycine, and threonine) in proteins accounts for ~95% of acetylated residues. We have found that a crude lysate from Saccharomyces cerevisiae mutant (aaa1) deficient in N(α)-acetyltransferase activity can effectively transfer an acetyl group to peptides containing NH2-terminal methionine but not to serine or alanine. This methionine N(α)-acetyltransferase has been extensively purified, and this purified enzyme can selectively transfer an acetyl group to various model peptides containing an NH2-terminal methionine residue and a penultimate aspartyl, asparaginyl, or glutamyl residue. Such specificity of N(α)-acetylation of methionine has been previously observed based on the analysis of eukaryotic protein sequences (Persson, B., Flinta, C., Heijne, G., and Jornvall, H. (1985) Eur. J. Biochem. 152, 523-527; Arfin, S. M., and Bradshaw, R.A. (1988) Biochemistry 27, 7979-7984). The identification of this methionine N(α)-acetyltransferase provides an explanation as to why two distinct classes of N(α)-acetylated proteins exist in nature: (i) those whose initiator methionine is acetylated and (ii) those whose penultimate residue is acetylated after cleavage of the initiator methionine.