ObjectiveTo explore the diagnostic value of ultrasound elastography (USE) combined with long non-coding RNA actin filament associated protein 1 anti-sense RNA 1 (AFAP1-AS1) mRNA in thyroid fine-needle aspiration (FNA) wash-out fluid for distinguishing benign from malignant thyroid nodules. MethodsThe patients with thyroid nodules who were treated in the Shenzhen Futian District Second People’s Hospital from January 2020 to June 2022 were collected. Before operation, the patients’ thyroid nodules were evaluated by the USE score and the AFAP1-AS1 mRNA in the thyroid FNA wash-out fluid was detected. The pathological result of the thyroid nodule after operation was as a gold standard for diagnosis of malignant thyroid nodules. The clinical diagnostic value of USE score combined with AFAP1-AS1 mRNA in the FNA wash-out fluid of the benign and malignant thyroid nodules were analyzed. ResultsA total of 174 thyroid nodules (124 patients) were detected in this study, of which 62 (45 patients) were histologically diagnosed as malignant. There was a statistical difference in the comparison of the composition ratio of USE score grading between the benign and malignant thyroid nodules (Z=8.82, P<0.001). The point of USE of the benign thyroid nodules was statistically lower than that of the malignant thyroid nodules [2.28±1.16 vs. 4.26±1.01, mean difference (MD) and 95% confidence interval (95%CI)=2.98 (2.76, 3.20), t=30.85, P<0.001]. The AFAP1-AS1 mRNA in the FNA wash-out fluid of the malignant thyroid nodules was statistically higher than that of the benign thyroid nodules [1.45±0.27 vs. 1.13±0.16, MD (95%CI)=1.45(1.39, 1.50), t=10.69, P<0.001]. Pearson correlation analysis showed that there was a positive correlation between the USE score of thyroid nodules and the expression of AFAP1-AS1 mRNA in the FNA wash-out fluid (r=0.58, P<0.001). The sensitivity and specificity of USE score in combination with expression of AFAP1-AS1 mRNA in the FNA wash-out fluid for diagnosing the malignant thyroid nodules by receiver operating characteristic (ROC) curve was 93.5% and 88.4% respectively. The area under the ROC curve (95%CI) was 0.91 (0.86, 0.96). Conclusion According to preliminary results of this study, USE score combined with AFAP1-AS1 mRNA in the thyroid FNA wash-out fluid is more sensitive and shows a potential diagnostic performance than USE score or AFAP1-AS1 mRNA detection alone for distinguishing benign from malignant thyroid nodules.