BackgroundThe Bethesda category III, AUS/FLUS, comprises a heterogeneous group of thyroid lesions with variable risk of malignancy (ROM). This study evaluates ROM in two subgroups of this category based on nuclear atypia and architectural atypia.MethodsCases in Bethesda category III were reported based on nuclear atypia (AUS) and architectural atypia (FLUS). ROM was calculated by comparing the cytologic diagnosis to the follow‐up histologic diagnosis.ResultsAmong the 610 Bethesda category III cases in this study, 306 (50.2%) and 304 (49.8%) cases were reported as AUS and FLUS, respectively. One hundred and eighty six of 306 AUS (60.8%) and 193 of 304 FLUS (63.5%) cases underwent surgical intervention. ROM of the cases in Bethesda category III was 12.8% if all cases were counted and 20.6% if only surgical cases were counted. When analyzing separately, ROM of AUS cases was 17.0% and 28.0% with all cases and surgical cases only, respectively. For FLUS cases, ROM was 8.6% and 13.5% with all cases and surgical cases only, respectively.ConclusionIn Bethesda category III, ROM in the cases with nuclear atypia was significantly higher than the cases with architectural atypia. Sub‐classifying the Bethesda Category III cases with nuclear atypia and architectural atypia, respectively may better stratify the ROM.