Objective:To explore the diagnostic efficacy of ultrasound-guided fine needle aspiration cytology(US-FNAC) for thyroid nodules ≥1 cm, and the effect of Hashimoto's thyroiditis(HT) on it. Methods:The clinical data of 1027 cases of thyroid nodules ≥ 1 cm were retrospectively analyzed. Two-dimensional ultrasound, US-FNAC and BRAFV600E gene testing were performed. The postoperative pathological results were used as the criterion. The two dimensional ultrasound examination, clinical characteristics, follow-up results, and BRAFV600E were used to diagnosis for unoperated patients. The diagnostic efficiency of US-FNAC in HT(+) group and HT(-) group was compared, and the factors affecting the diagnostic efficiency were analyzed. Results:Of the 1027 nodules, the cytological results were nondiagnostic/unsatisfactory in 73 nodules(7.1%), benign in 282(27.5%), atypia of undetermined significance/follicular lesion of undetermined significance in 230(22.4%), follicular neoplasm/suspicious for a follicular neoplasm in 20(1.9%), suspicious for malignancy in 120(11.7%), and malignant in 302(29.4%). 515 cases underwent surgery. Among them, 495 were malignant and 20 were benign. 512 cases continued to be followed up without surgery, and the BRAFV600E of them were wild type. Combined with the two dimensional ultrasound examination, clinical features, and follow-up results, they were judged to be benign. The accuracy, sensitivity, specificity, positive predictive value, negative predictive value, false positive rate and the false negative rate the of US-FNAC were 98.7%, 98.4%, 99.3%, 99.5%, 97.5%, 0.7% and 1.6%, respectively. The accuracy, sensitivity and negative predictive value of the HT(+) group were 95.5%, 95.4% and 82.8%, respectively, which were lower than that of HT(-) group (99.5%, 99.4%, 99.2% )(P=0.001, 0.018, P<0.001). The false negative rate of the HT(+) group was 4.6%, higher than 0.6% of the HT(-) group(P=0.018), and HT was an risk factor for increased FNR(OR=7.596, 95%CI: 1.452-39.740). Conclusion:US-FNAC is an effective method for the diagnosis of thyroid nodules and it has high sensitivity and specificity in ≥ 1 cm nodules. However, the combination of HT reduces the diagnostic accuracy and HT is a risk factor for increased false negative rate.