Saliva is secreted by salivary glands and performs a variety of functions, including mouth cleaning and protection, antibacterial activity, and digestion. With the rapid progress in salivaomics, saliva became recognized as a potential pool of biological markers. Being a non-invasive and safe source, saliva is a potential substitute for blood in diagnosis and prognosis of diseases. This review summarizes the latest advancement in saliva-related studies and presents the potential value of saliva in early diagnosis of oral diseases, such as dental caries, periodontal disease, cancer, diabetes, and other systemic disorders. Saliva biomarkers can reveal changes ranging from changes in biochemical index, DNA, RNA, and proteins to the diversification of microbiota structure. By integrating recent data, this paper discusses the clinical significance and application prospect of saliva in early diagnosis of diseases and in translational and precision medicine.