Objectives: To evaluate accuracy of FDG-PET CT in prediction of persistent disease in head and neck cancer cases and to determine prognostic value of metabolic tumor response. Materials and Methods: Between 2009 and 2011, 46 patients with squamous cell carcinoma of head and neck receiving PET-CT were treated with definitive radiotherapy, with or without chemotherapy. There were 29 nasopharyngeal, 11 hypopharyngeal, 3 oropharyngeal and 3 laryngeal cancer patients, with a median age of 50.5 years (range 16-84), 32 males and 14 females. All patients were evaluated with PET-CT median 3-5 months (2.4-9.4) after completion of radiotherapy. Results: After a median 20 months of follow up, complete metabolic response was observed in 63% of patients. Suspicious residual uptake was present in 10.9% and residual metabolic uptake in 26.0% of patients. The overall sensitivity, specificity, positive predictive value and negative predictive value of FDG-PET-CT for detection of residual disease was 91% and 81%, 64% and 96% respectively. Two year LRC was 95% in complete responders while it was 34% in non-complete responders. Conclusions: FDG PET CT is a valuable tool for assessment of treatment response, especially in patients at high risk of local recurrence, and also as an indicator of prognosis. Definitely more precise criteria are required for assessment of response, there being no clear cut uptake value indicating residual disease. Futhermore, repair processes of normal tissue may consume glucose which appear as increased uptake in control FDG PET CT.