The diagnostic category of atypia of undetermined significance (AUS) in the Bethesda System for reporting the results of thyroid fine-needle aspirations (FNAs) is intended to encompass findings associated with a low risk of malignancy. It is unclear if there are patterns within this evolving, heterogeneous category associated with differing risk of malignancy that might warrant alternative classification or clinical management. Therefore, a retrospective review of 512 AUS FNAs from January 2005 to May 2009 was done. Most malignancies associated with AUS were papillary carcinoma (86/96 [90%]), of which 85% (73/86) were follicular variants. Atypia qualifiers were correlated with the follow-up rate of malignancy. The risk of malignancy for architectural atypia alone was approximately half that observed for cytologic, both cytologic and architectural, or unspecified atypia. Architectural atypia alone was less likely to be papillary carcinoma and more likely to be follicular adenoma. The lower risk of malignancy associated with isolated architectural atypia compared with other patterns of AUS should be considered in clinical decision making and in future management guidelines.