We performed a retrospective review of (18)F-fluorodeoxyglucose positron emission tomography (FDG-PET) examination to determine the prevalence of thyroid FDG-PET incidentaloma in a patient group evaluated for metastasis of cancer and in a group of healthy subjects who underwent voluntary cancer screening. We also evaluated the risk of malignancy in focal thyroid FDG-PET incidentaloma and its association with standard uptake values (SUVs) (maximum and greater than 0.75 threshold). A total of 1330 subjects underwent FDG-PET for metastasis evaluation (n = 999) and cancer screening (n = 331). Twenty-nine of 1330 subjects (2.2%) showed focal (n = 21) or diffuse (n = 8) thyroid FDG-PET incidentaloma. There was no significant difference in the prevalence of thyroid FDG-PET incidentaloma between the two groups (19 of 999 vs. 10 of 331; P > 0.05). Four of 15 focal incidentalomas (26.7%) whose histological diagnoses were available showed papillary thyroid cancer. The maximum SUV (16.5 +/- 4.70) and greater than 0.75 threshold SUV (14.2 +/- 5.3) of malignant lesions were significantly higher than those of benign tumors (6.5 +/- 3.8 and 4.9 +/- 3.0; P < 0.05). In conclusion, thyroid FDG-PET incidentaloma has prevalence of 2.2%, and its prevalence was not different according to the purpose of the FDG-PET. The focal thyroid FDG-PET incidentaloma carries a high risk of malignancy, especially in cases with high SUVs. Therefore, focal thyroid FDG-PET incidentaloma with high SUVs warrants a pathological diagnostic procedure if it changes a patient's treatment plan or prognosis.