Saliva is a complex fluid that consists of 99% water and 1% organic and inorganic substances. Proteomics and genomics technologies are used to develop biological markers in studies using saliva samples, which are involved in many biological processes and may be obtained by completely noninvasive methods. Saliva is accepted to be a more advantageous diagnostic fluid than serum since it can be collected easily and therefore it is suggested to be a rapid and cost effective method when determining the presence of systemic diseases in large populations. Saliva samples have been used for dental caries risk assessments and diagnosis of periodontal diseases for 20 years; recently these samples are used for the diagnosis of systemic diseases and therapeutic drug monitoring. Currintly, the pathologies that may be diagnosed through saliva samples include malignant disorders, autoimmune and infectious diseases. The development of rapid human immunodeficiency virus (HIV) tests that are based on the presence of specific antibodies in saliva is a major development in this area. Today the systemic levels of steroids such as cortisol, dehydroepiandrosterone (DHEA), testosterone, estradiol, estriol and progesterone can be accurately detected through saliva samples. Saliva is also used for the diagnosis of Alzheimer diseases, rheumatoid arthritis and Sjogren's syndrome. The increasing use of diagnostic markers in saliva for monitoring systemic diseases has led researchers to investigate saliva for the presence of cancer biomarkers. Recently, in a study where saliva samples from healthy subjects and subjects with head-neck cancer were compared, it was reported that an increase in mRNA level was observed for specific proteins in cancer patients. Additionally the codon 63 mutation in p53 gene is accepted as a diagnostic marker for oral squamous cell carcinoma. The aim of the present article was to provide some knowledge on the structure and diagnostic applications of saliva.