The detection of distant metastases and second primary tumours at the time of initial evaluation changes the prognosis and influences the selection of treatment modality in patients with HNSCC. Until recently chest CT was the single most effective test to screen for distant metastases in HNSCC patients. In this observational cohort study we prospectively compared the yield of whole body (18)FDG-PET and chest CT to detect distant metastases and synchronous primary tumours. The results of whole body (18)FDG-PET and chest CT were analysed in 34 consecutive HNSCC patients with previously established risk factors for the presence of distant metastases. Four patients were diagnosed with distant metastases or second primary tumours: CT as well as (18)FDG-PET identified one patient with lung metastases and another with primary lung cancer. In addition, (18)FDG-PET detected second primary tumours in two patients (hepatocellular carcinoma and abdominal adenocarcinoma). However increased uptake sites at (18)FDG-PET in lung, liver and pelvis in five patients were not confirmed by other imaging modalities. The added value of whole body (18)FDG-PET versus chest CT was to identify unknown malignancy in 6% of the patients. Confirmation of positive (18)FDG-PET findings is feasible and necessary.