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This study aimed to evaluate the usefulness of the biphasic 2-deoxy-2-[18 F]fluoro-D-glucose positron emission tomography/computed tomography ([18 F]FDG PET/CT) examinations in terms of distinguishing benign and malignant lesions within the pharynx. 139 patients underwent sequential biphasic [18 F]FDG PET/CT examinations at 60 and 90 minutes (min) post intravenous injection (p.i.) of the [18 F]FDG. We evaluated the metabolic activity of 93 malignant lesions and 59 benign findings within pharynx as well as 70 normal blood vessels. We evaluated the maximal and mean standardized uptake value (SUVmax, SUVmean) and the retention index (RI-SUVmax). We used the receiver operating characteristics (ROC) analysis to obtain the prognostic metabolic indices cut-off which may differentiate between benign and malignant lesions. The SUVmax value cut-off at 60 and 90 min p.i. differentiating between normal and abnormal metabolic activity in the pharynx was 1.9 and 2.0, respectively. When compared benign and malignant lesions, the SUVmax on initial and delayed scans were 3.1 and 3.6, respectively. In this material, the increase of the SUVmax value over time of 1.7% suggested abnormality, while RI-SUVmax of 5.7% indicated malignant etiology. The biphasic [18 F]FDG PET/CT study protocol is useful in better stratification of normal and abnormal glucose metabolism activity in the pharynx.