Objective To investigate the prevalence of the suspicious primary thyroid disease incidentally detected by 18F-FDG PET/CT and to explore the diagnostic value between malignant and benign thyroid disease. Methods During November 2010 to May 2013, 2569 patients were suspected primary thyroid disease via 18F-FDG PET/CT scan．Among them, 1219 patients were proved hyper-metabolic lesions. Sixty-seven patients were conformed via histopathology or clinical follow-up. Then, these patients were analyzed with metabolism, PET and CT imaging to reveal the characteristic features between malignant and benign. Results Malignant rate of hypermetabolic thyroid nodules was significantly different from that of diffuse hypermetabolic thyroid （P<0.01）. The SUVmax value of malignant and benign for the patients with single hypermetabolic thyroid nodule were 6.63±4.49 and 3.07±1.42, respectively (t=2.436，P=0.035). The SUVmax value of malignant and benign for the patients with multiple nodules single hypermetablic focus were 5.72±2.47 and 3.37±0.74, respectively (t=1.870，P=0.151). No statistics difference of SUVmax value was found between malignant group and benign group with multiple hypermetabolic thyroid nodules. Conclusion Focal hypermetabolic thyroid nodules detected via 18F-FDG PET/CT come with high malignant rate. Differential diagnosis between malignance and benign can be conducted by the SUVmax value.