The early detection of recurrences after surgical or radiation treatment of squamous cancers of the head and neck is often difficult. A rise in circulating tumor marker levels such as SCCA and CEA often precedes the clinical appearance of recurrences by about several months. The combined analysis of SCCA and CEA can facilitate the early detection of local relapse or distant recurrence and can therefore accelerate specific diagnostic and/or therapeutic procedures. Therefore, after primary therapy of locally advanced head and neck cancers, the combined analysis of SCCA and CEA normally every 3-6 months can be recommended. Molecular markers give increasing insight into tumor biology, prognosis and response to chemotherapy, radiation and molecular targeted therapies. Biomarkers require a careful validation before being implemented into clinical decision making, but promising markers such as EGFR, p53 and HPV oncogene may become important stratification factors for individualized tumor treatment algorithms.