Besides their structural catalytic and diverse regulatory functions, proteins are also precursors of many important biological compounds essential for normal functioning of humans. Many of these compounds may be used as markers for identification of specific pathological states. A comprehensive knowledge about the metabolism of salivary proteins and the mechanisms of action of their metabolites allowed the development of effective treatment for many disorders. However, it should not be forgotten that in some pathological conditions, these compounds not only could be involved in the pathogenesis but also could be used as tool in the prediction of many diseases. This paper is a review of the published literature on selected salivary proteins in the context of the physiological processes of the human body and chosen chronic disorders, such as diabetes, diabetic nephropathy, mucositis, oral mycoses and caries.