Protein-related homocysteine (Hcy) metabolism generates Hcy-thiolactone thioester (1), N-Hcy-protein adducts (2), and N-Hcy-Lys) isopeptide (3). (1) is generated in an enzymatic error-editing reaction in protein biosynthesis when Hcy is erroneously selected in place of methionine by methionyl-tRNA synthetase. The Hcy editing reaction and the biosynthesis of (1) are universally conserved from bacteria to humans. (2) is formed in a chemical reaction of (1) with -amino groups of protein lysine residues in mice and humans. (3) is a product of proteolytic degradation of (2) that occurs in mice and humans. Chemical biology and pathophysiology of these metabolites is summarized in this review.