Abstract Background The Bethesda system (TBS) for reporting thyroid cytopathology recommends an “atypia of undetermined significance (AUS)” rate of 10%. Recent data suggest that this category might be overused when the rate of cases with molecular positive results is low. As a quality metric, we calculated the AUS and positive call rates for our cytology lab and each cytopathologist. Methods A retrospective analysis of all thyroid cytology cases in a 4.5-year period was performed. Cases were stratified by TBS category, and molecular testing results were collected for indeterminate categories. The AUS rate was calculated for each cytopathologist (CP) and the laboratory. The molecular positive call rate (PCR) was calculated with and without the addition of currently negative to the positive results obtained from the ThyroSeq report. Results 7,535 cases were classified as non-diagnostic 7.6%, benign 69%, AUS 17.5%, follicular neoplasm / suspicious for follicular neoplasm 1.4%, suspicious for malignancy 0.7 %, and malignant 3.8%. The AUS rate for each cytopathologist ranged from 9.9-36.8%. The overall PCR for the cytology laboratory was 24% (range 13-35.6% per CP). When including cases with currently negative results, the PCR increased to 35.5% for the cytology laboratory (range 13-42.6% per CP). Comparison analysis indicates a combination of overcalling benign cases and, less frequently, under calling of higher TBS category cases. Conclusions The AUS rate in the context of PCR is a useful metric to assess cytology laboratory and cytopathologists’ performance. Continuous feedback on this metric could help improve the overall quality of reporting thyroid cytology.