Pepsins are aspartate proteases and are the major proteolytic enzymes found in the gastric juice of vertebrates. As such, they are vital both in normal digestive function and innate protection of the gut from infection. Adult human gastric juice contains two groups of pepsins, A and C and the genes for these are located on different chromosomes. Pepsins catalyse the hydrolysis of peptide bonds via nucleophilic attack facilitated by the aspartates at the active site acting as an acid/base pair. The active enzyme pepsin is generated from an inactive zymogen (pepsinogen) on exposure to a pH below 5, producing a metastable pepsin molecule as a result of autocatalysis. Pepsins are irreversibly inactivated by exposure to pHs above neutral. If they are subsequently returned to an acidic pH, a mis-folded and inactive pepsin results. Pepsin activity can also be greatly reduced by the presence of specific inhibitors such as pepstatins (e.g. 16 amino acid peptides isolated from Streptomyces), and non-specific inhibitors, like alginates (polyuronic biopolymers used in anti-reflux therapies). Pepsin is an important biomarker of reflux of gastric juice into the aerodigestive tract and it is an important damaging agent up to pH 6. Pepsin will always be present in gastric refluxate, whereas for bile to be present, duodenal reflux into the stomach must first occur. Current methodology (ELISA and proteolytic activity assays) with the required sensitivity is available to measure pepsin, whereas the currently available enzymatic assay for bile acids is not sensitive enough for all reflux related applications.