The human salivary peroxidase system (SPS) contributes in several ways to the maintenance of good oral health. The SPS is one of the non-immunoglobulin defense factors which regulate the quantity and species distribution of oral micro-organisms. The SPS also prevents toxic accumulations of hydrogen peroxide (H2O2) and it inactivates many carcinogenic and mutagenic compounds. The salivary glands secrete a peroxidase enzyme (salivary peroxidase) as well as the thiocyanate ion (SCN-, derived from diet). The enzyme catalyzes the oxidation of SCN- by hydrogen peroxide (H2O2). The H2O2 is excreted by oral bacteria and by host cells in amounts which vary with the state of cellular metabolism, the diet and other factors. Oxidized forms of SCN- temporarily inhibit the growth, respiration and metabolism of most species of oral bacteria. The major oxidized form generated in the mouth is the hypothiocyanite ion (OSCN-) which must reach a minimum threshold concentration before bacterial inhibition occurs. This threshold concentration varies from species to species. The concentration of OSCN- in the mouth rises and falls with the availability of H2O2. This natural rise and fall, together with bacterial variation in sensitivity to OSCN- inhibition, suggests a role for the SPS in the regulation of the oral microflora. As a result of the rapid consumption of H2O2 by the SPS, host cells are protected from a toxic build up of this potent oxidizing agent. The major product of the reaction, OSCN-, does not harm human cells. Many carcinogenic and mutagenic compounds may serve as substrates for the SPS and be oxidized to less harmful compounds.