Saliva is mainly composed of secretions from salivary glands, gingival crevicular fluid, and mucosal transudate. Saliva provides genetic information originating from DNA or RNA of human oral microorganisms located in oral local tissue and other parts of the body. Saliva has an important role in systematically detecting changes of messenger RNA(mRNA) or proteins. As a non-invasive source of complex genetic information of human and oral microbes, extensive studies on saliva have been conducted, such as salivary genomics, transcriptomics, proteomics, microbiomics, metabolomics and miRNA. This review summarized the latest developments of salivaomics and addressed the potential value of saliva in the early diagnosis of oral diseases, such as dental caries, periodontal disease, Sjögren syndrome, oral cancer, head and neck tumors, oral candidiasis and other systemic disorders or viral infections.