This review summarizes the current data on the effects of natural products on various oral diseases, together with their basic biological activities. We have focused on polyphenols and their secondary metabolites, such as tannins, lignins and flavonoids, and their modulating factors, including saliva proline-rich proteins. These substances are found in a wide variety of plant sources such as vegetables, herbs, nuts and teas, and effectively reduce the incidence of carcinogenesis in the oral cavity, inhibit plaque growth and adsorption of oral bacteria, and inhibit the replication of various viruses. The mechanism of their action includes: the direct inactivation of the bacteria and viruses, inhibition of their replication enzymes, induction of apoptosis in tumor cells, stimulation of monocytes/macrophages to produce cytokines, and stimulation of myeloperoxidase-dependent iodination of neutrophiles. Polyphenols showed biphasic actions, acting as antioxidants at lower doses, but acting as prooxidants at higher doses. The development and progression of oral diseases might be modified not only by these natural products, but also by interaction with saliva, proline-rich proteins, antioxidants, metals and dental materials.