Magnetic resonance spectroscopy of biomolecules has recently gained attention for clinical diagnosis. Its combination with saliva collection and analysis can promote early disease detection and monitoring, by identifying biomarkers of specific underlying pathology or disease as detected in saliva. With this novel, non-invasive technique, certain salivary biomarkers have been linked to dental and periodontal tissues pathology, as well as to specific head and neck cancer malignancies. At present, diagnostic biomarkers are still in need for further identification (e.g., diagnosis and monitoring of Sjögren's syndrome), and nuclear magnetic resonance spectroscopy has been found to be a promising technique to compliment the current analytic methodology. Moreover, this article reports on the various data collection and analysis parameters used in the literature. Protocol standardization is yet to be established not only for the laboratory procedures, but also for the clinical sample collection. Herein, we review the current status of utilizing nuclear magnetic resonance in order to further support data on health associated biomarkers, and we also propose a saliva sampling scheduling protocol with the potential to be used in the clinical and experimental setting for standardization of the testing methodology.