Amino acids in the luminal fluid of the small intestine, which originate from dietary and endogenous proteins after digestion, can be utilized by the microorganisms collectively known as the intestinal microbiota present within this fluid. Conversely, experimental arguments suggest that a part of amino acids produced by the intestinal microbiota is absorbed and used by the host. However, the amplitude of this exchange between the intestinal microbiota and lodging host (and vice versa) is not known. A minor part of the amino acids that are absorbed through enterocytes is metabolized during the transfer from the luminal fluid to the bloodstream in a context of rapid epithelium renewal. In enterocytes, amino acids are used for protein, DNA, and RNA syntheses. In these cells, specific amino acids, mainly glutamine and glutamate, serve as sources of ATP required for amino acid transport and further anabolism. Specific amino acids are metabolized within enterocytes for local functions. For instance, nitric oxide is produced from arginine while glutathione is produced from glutamate, cysteine, and glycine. Both nitric oxide and glutathione exert protective functions on the intestinal epithelium. Amino acid utilization in enterocytes corresponds also to interorgan metabolism, notably between intestine and liver, and between intestine and kidney. Also, some specific amino acids emerge as potential stimulant for the secretion of hormones by the enteroendocrine cells.