To evaluate the prevalence of thyroid FDG-PET/CT incidentalomas and the risk of malignancy in focal findings. A retrospective study of 3,062 PET scans was performed between 05/2006 and 09/2009. Prevalence of thyroid incidentalomas, risk of malignancy and correlation between standard uptake value (SUV) and cancer risk were analysed. The overall prevalence of thyroid incidentalomas was 2.4%. 71% showed a focal and 29% a diffuse uptake. In the focal uptake group, the diagnosis was clarified in 79% with cytology/histology. In 23.8% of the patients with a focal uptake, a malignant lesion was found. Diffuse uptake was predominantly associated with autoimmune thyroiditis. There was no statistically significant difference in the SUVmax between benign and malignant focal lesions (p = 0.0982). Patients with incidental focal uptake in the thyroid during FDG-PET/CT bear a considerable risk of malignancy and should undergo cytologic clarification of the diagnosis.