Lysine is an essential amino acid that serves as a building block in protein synthesis. Beside this, lysine's metabolic activity has only recently been unraveled. Lysine metabolism is tissue specific and is linked to several renal, cardiovascular and endocrinological diseases through human metabolomics datasets. As a free molecule, lysine takes part in antioxidant response, engages in protein modifications and its chemistry shapes both proteome and metabolome. In the proteome, it is an acceptor for a plethora of posttranslational modifications. In the metabolome it can be modified, conjugated and degraded. Here, we provide an update on integrative physiology of mammalian lysine metabolites such as α-aminoadipic acid, saccharopine, pipecolic acid, and lysine conjugates such as acetyl-lysine, and sugar-lysine conjugates such as advanced glycation end products. We also comment on their emerging associative and mechanistic links to renal disease, hypertension, diabetes and cancer.