The 5-year survival rates for cases of head and neck squamous cell carcinoma (HNSCC) are only some 60%, mainly because 20%-40% of the patients develop a local relapse in the same or an adjacent anatomic region, even when the surgical margins are histologically tumour-free. Tumours are often discovered in an advanced stage because of the lack of specific symptoms and the diagnostic difficulties. The more advanced the stage of the tumour, the more invasive the diagnostic and treatment interventions needed. An early molecular diagnosis is therefore of vital importance in order to increase the survival rate. The aim of this study was to develop an efficient rapid and sensitive mass spectrometric method for the detection of differentially expressed proteins as tumour-specific biomarkers in saliva from HNSCC patients. Whole saliva samples were collected from patients with HNSCC and from healthy subjects. The proteins were profiled by using SDS PAGE, MALDI TOF/TOF mass spectrometry and the Mascot database search engine. Several potential tumour markers were identified, including annexin A1, beta- and gamma-actin, cytokeratin 4 and 13, zinc finger proteins and P53 pathway proteins. All of these proteins play a proven role in tumour genesis, and have not been detected previously in saliva. Salivary proteomics is a non-invasive specific method for cancer diagnosis and follow-up treatment. It provides facilities for the readily reproducible and reliable detection of tumours in early stages.