The proper diagnosis is a critical factor to reduce further disturbances at the early stage of the disease and plays an important role in increasing the success rate of the therapy. The traditional diagnostic tools such as biopsy or blood collection are always associated with patient’s discomfort, the possibility of infections and time-consuming procedures. This article describes the non-invasive and easily accessible saliva as a source of numerous molecular biomarkers. The salivary fluid can provide information about the pathological changes not only in the oral area but also in other parts of the body, therefore salivary tests may be promising tools for risk prediction and treatment monitoring of many disorders.