Purpose: FDG avid thyroid incidentalomas pose a diagnostic challenge due to their potential for malignancy. This study evaluates the malignancy rates in FDG avid thyroid nodules, stratified by fine needle aspiration (FNA) cytology results. Methodology: A multi-centre, retrospective analysis was conducted on patients with FDG-avid thyroid incidentalomas who underwent surgical resection in Western Australia between 2012 and 2023. Overall malignancy rates were reported in addition to malignancy rates stratified by pre-operative cytology result. Multivariable logistic regression was used to assess the utility of patient age, gender and nodule size for predicting malignancy in FDG-avid thyroid incidentaloma. Results: Among the 258 patients with FDG avid thyroid incidentalomas, malignancy rates according to FNA results were: Bethesda I (15.4%), Bethesda II (11.1%), Bethesda III (29.1%), Bethesda IV (34%), Bethesda V (83.3%), and Bethesda VI (98.3%). There was an overall malignancy rate of 48.1%, predominantly papillary thyroid carcinoma. No significant differences in malignancy were observed concerning age, gender, or nodule size. Conclusion: FDG avid thyroid nodules exhibit a significantly higher risk of malignancy, especially in Bethesda categories III to VI.