The risk of malignancy (ROM) in FDG-avid thyroid incidentalomas varies between studies, which may be contributed by discordance between the anatomical localization depicted on 18FDG-PET/CT and by histopathological examination. The purpose was to ensure anatomical congruity between the index tumour identified by 18FDG-PET/CT and the histopathological examination, in order to assess the risk of malignancy (ROM) in PET-positive and PET-negative thyroid nodules. Further, preoperative characteristics indicative of thyroid malignancy were identified.Thirty-two patients referred to thyroid surgery were prospectively included. 18FDG-PET/CT, fine-needle aspiration biopsy and thyroid ultrasonography examination were performed in all participants. The exact anatomical localization of the index nodule was established by histopathological examination to ensure concordance with the 18FDG-PET/CT finding.Forty thyroid nodules were included. Malignancy was identified in 10 of 28 PET-positive nodules and in 1 of 12 PET-negative nodules, resulting in a ROM of 36% and 8%, respectively. A Hurtle cell neoplasm was found in 50% of patients with a benign nodule and a PET-positive scan. One PET-negative nodule represented a papillary microcarcinoma. In PET-positive nodules, hypoechogenicity, irregular margins, and pathological lymph nodes on thyroid ultrasonography were characteristics associated with malignancy.In this study-ensuring anatomical congruity between PET-findings and the histopathological examination-the risk of malignancy in PET-positive thyroid nodules was 36%. A low ROM was seen in thyroid nodules without suspicious ultrasonographic findings, independent of the 18FDG-PET/CT result.NCT02150772 registered 14th of April 2014.