The risk of malignancy is considered to be 10% to 30% for cases of thyroid nodules with atypia or follicular lesion of undetermined significance (AUS/FLUS). However, only a minority of patients with AUS/FLUS undergo surgery; therefore, the risk of malignancy might be overestimated due to selection bias. To overcome this problem, we categorized cases of thyroid nodules with AUS/FLUS using the ultrasound risk stratification system (US-RSS) to calculate the malignancy rate and identify the patients most suitable for surgical treatment.In this retrospective observational study, we subcategorized 382 pathologically confirmed thyroid nodules with AUS/FLUS using current US-RSSs (American Thyroid Association, Korean-Thyroid Imaging Report and Data System, American College of Radiology-Thyroid Imaging, Reporting and Data System, European Thyroid Imaging Report and Data System) and calculated the malignancy rate. Additionally, cases of nodules with AUS/FLUS were categorized according to their cytological subtypes, and the malignancy rate was calculated.Current US-RSSs showed good or moderate agreement among them. The overall malignancy rate for thyroid nodules with AUS/FLUS was 38.7%. On categorization of the nodules with AUS/FLUS, the malignancy rates were found to be 60% to 67.5% for the high suspicion category, 32.2-36.6% for the intermediate suspicion category, and 12.4% to 16.3% for the low suspicion category. The malignancy rate for nodules with cytologic atypia was significantly higher than that for nodules with architectural atypia, especially in the intermediate suspicion category.Categorization of thyroid nodules with AUS/FLUS using current US-RSSs helps to determine the optimal course of management of patients, especially when combined with cytological subtype characterization.