Saliva contains a variety of biomolecules, including DNA, coding and noncoding RNA, proteins, metabolites and microbiota. The changes in the salivary levels of these molecular constituents can be used to develop markers for disease detection and risk assessment. Use of saliva as an early-detection tool is a promising approach because collection of saliva is easy and noninvasive. Here, we review recent developments in salivary diagnostics, accomplished using salivaomics approaches, including genomic, transcriptomic, proteomic, metabolomic and microbiomic technologies. Additionally, we illustrate the mechanisms of how diseases distal from the oral cavity can lead to the appearance of discriminatory biomarkers in saliva, and discuss the relevance of these markers for translational and clinical applications.