ObjectivesThis study aims to investigate the efficacy of a computer-aided diagnosis (CAD) system in distinguishing between benign and malignant thyroid nodules in the context of Hashimoto’s thyroiditis (HT) and to evaluate the role of the CAD system in reducing unnecessary biopsies of benign lesions.MethodsWe included a total of 137 nodules from 137 consecutive patients (mean age, 43.5 ± 11.8 years) who were histopathologically diagnosed with HT. The two-dimensional ultrasound images and videos of all thyroid nodules were analyzed by the CAD system and two radiologists with different experiences according to ACR TI-RADS. The diagnostic cutoff values of ACR TI-RADS were divided into two categories (TR4 and TR5), and then the sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) of the CAD system and the junior and senior radiologists were compared in both cases. Moreover, ACR TI-RADS classification was revised according to the results of the CAD system, and the efficacy of recommended fine-needle aspiration (FNA) was evaluated by comparing the unnecessary biopsy rate and the malignant rate of punctured nodules.ResultsThe accuracy, sensitivity, specificity, PPV, and NPV of the CAD system were 0.876, 0.905, 0.830, 0.894, and 0.846, respectively. With TR4 as the cutoff value, the AUCs of the CAD system and the junior and senior radiologists were 0.867, 0.628, and 0.722, respectively, and the CAD system had the highest AUC (P < 0.0001). With TR5 as the cutoff value, the AUCs of the CAD system and the junior and senior radiologists were 0.867, 0.654, and 0.812, respectively, and the CAD system had a higher AUC than the junior radiologist (P < 0.0001) but comparable to the senior radiologist (P = 0.0709). With the assistance of the CAD system, the number of TR4 nodules was decreased by both junior and senior radiologists, the malignant rate of punctured nodules increased by 30% and 22%, and the unnecessary biopsies of benign lesions were both reduced by nearly half.ConclusionsThe CAD system based on deep learning can improve the diagnostic performance of radiologists in identifying benign and malignant thyroid nodules in the context of Hashimoto’s thyroiditis and can play a role in FNA recommendations to reduce unnecessary biopsy rates.