Heat and alkali treatments of foods, widely used in food processing, result in the formation of dehydro and cross-linked amino acids such as dehydroalanine, methyldehydroalanine, beta-aminoalanine, lysinoalanine (LAL), ornithinoalanine, histidinoalanine (HAL), phenylethylaminoalanine, lanthionine (LAN), and methyl-lanthionine present in proteins and are frequently accompanied by concurrent racemization of L-amino acid isomers to D-analogues. The mechanism of LAL formation is a two-step process: first, hydroxide ion-catalyzed elimination of H(2)S from cystine and H(2)O, phosphate, and glycosidic moieties from serine residues to yield a dehydroalanine intermediate; second, reaction of the double bond of dehydroalanine with the epsilon-NH(2) group of lysine to form LAL. Analogous elimination-addition reactions are postulated to produce the other unusual amino acids. Processing conditions that favor these transformations include high pH, temperature, and exposure time. Factors that minimize LAL formation include the presence of SH-containing amino acids, sodium sulfite, ammonia, biogenic amines, ascorbic acid, citric acid, malic acid, and glucose; dephosphorylation of O-phosphoryl esters; and acylation of epsilon-NH(2) groups of lysine. The presence of LAL residues along a protein chain decreases digestibility and nutritional quality in rodents and primates but enhances nutritional quality in ruminants. LAL has a strong affinity for copper and other metal ions and is reported to induce enlargement of nuclei of rats and mice but not of primate kidney cells. LAL, LAN, and HAL also occur naturally in certain peptide and protein antibiotics (cinnamycin, duramycin, epidermin, nisin, and subtilin) and in body organs and tissues (aorta, bone, collagen, dentin, and eye cataracts), where their formation may be a function of the aging process. These findings are not only of theoretical interest but also have practical implications for nutrition, food safety, and health. Further research needs are suggested for each of these categories. These overlapping aspects are discussed in terms of general concepts for a better understanding of the impact of LAL and related compounds in the diet. Such an understanding can lead to improvement in food quality and safety, nutrition, microbiology, and human health.