Molecular markers can be used for the diagnostic (early detection, assessment of tumor extent, detection of residual disease), for the prognostic (disease classification and therapeutic indications), for the treatment (treatment target and predictive factors of tumor response to treatment) and for the prevention (identification of the at-risk population and chemoprevention). Molecular markers have to be validated by prospective studies using appropriate methods. Currently, no molecular marker is used in routine practice for the management of upper aerodigestive tract cancers, but new techniques are being developed to analyze simultaneously tens of thousands of markers; they should expand our knowledge of the biology of these cancers.