Although very attractive for noninvasive specimen collection, saliva has not yet been considered a relevant bodily fluid for the diagnosis and prognosis of diseases. The functional roles of specific salivary peptides and proteins have also not yet been studied in detail. Recent proteomic analysis of human whole saliva has shown that salivary biomarkers could contribute to the detection of local and systemic diseases, provided the standardization of proper sampling procedures exists. Recently, interesting and novel functions for different families of specific secretory peptides and proteins have been demonstrated, which could be a basis for the design of peptidomimetics with relevant biotechnological applications. In this review, we focus on the most recent advances in analysing salivary proteins and their potential application in biotechnology.