The D-enantiomers of L-amino acids are non-proteinogenic but widely present in foods. This is due to spontaneous racemization or processing, such as heating or alkali treatment, leading to substantial dietary exposure. Additional exposure to D-amino acids (D-AAs) comes from the human microbiota; D-AAs are present in bacterial surface proteoglycans, essential for bacterial competition and growth. Humans and other mammals have a complex set of genes for D-AA transport and degradation, and capacity to synthesize several D-AAs. Free D-AAs are present at low levels in human tissues and body fluids, yet they are apparently of considerable physiological and pathological importance. Amino acid transport regulates their presence and favors specific D-AAs, e.g. D-serine, D-aspartate, D-cysteine, and D-glutamate, over many others. Some of these D-AAs interact with the ubiquitous glutamate-gated Ca²⁺ channels, affecting signaling functions in most organs, especially the intestine, kidney, and brain. Consequently, the exposures, synthesis, local and systemic transport of D-AAs could be much more biologically important in humans than previously assumed, likely playing a role in gut-organ signaling and in many degenerative diseases.