Objectives: Ultrasound-guided fine-needle aspiration (FNA) is the most accurate and economical means for the differential diagnosis of thyroid nodules, but false negative results also existed. This study aimed to predict the false negative results of FNA, reduce the missed diagnosis and improve the current management strategy of thyroid nodules. Methods: A total of 1232 consecutive patients with thyroid nodules who received FNA and BRAF V600E detection were adopted. All patients received both CUS (conventional ultrasound) and SWE (shear wave elastography) examinations and characteristics of these thyroid nodules were analyzed to evaluated the diagnostic performances of risk factors for malignancy.Results: Finally, 26 nodules with benign cytology and BRAF V600E mutations were enrolled. Undefined boundary, microcalcification and E max ratio > 1.49 were risk factors for malignancy (P<0.05), and the area under the receiver operating curve (ROC) of above CUS features and elastic value were 0.817 (95% CI: 0.617, 0.940), 0.792 (95% CI: 0.588, 0.925) and 0.792 (95% CI: 0.617, 0.940) respectively. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were 80.0%, 83.3%, 94.1%, 55.6% and 80.7% for undefined boundary, 75.0%, 83.3%, 93.8%, 50.0% and 76.9% for microcalcification and 75.0%, 83.3%, 93.8%, 50.0% and 76.9% for E max ratio > 1.49 respectively. There was no difference between benign and malignant nodules in the patient age, sex and nodule sizes (P>0.05).Conclusions: Undefined boundary, microcalcification and E max ratio > 1.49 were risk factors for malignancy in benign cytology nodules. When FNA results were benign but above characteristics could be found in the thyroid nodules with BRAF V600E mutation, further clinical decisions should be carried out to reduce the missed diagnosis.