Background: Atypia/follicular lesion of undetermined significance (A/FLUS) is a new category in the Bethesda System for Reporting Thyroid Cytopathology (BSRTC) for which repeat fine-needle aspiration biopsy (FNAB) is recommended. Methods: A retrospective review was completed to evaluate the impact of the BSRTC on management of nodular thyroid disease. Patients were divided into pre-BSRTC and BSRTC groups. A comparative analysis of cytopathologic diagnoses and rates of repeat FNAB and malignancy was completed. Results: FNAB was performed in 730 patients: 337 pre-BSRTC and 393 BSRTC. There was a decrease in follicular/Hürthle cell neoplasm (FN/HCN; 9.5% vs 3.6%, P =.001) but no difference in the rate of malignancy (6.5% vs 6.4%, P = 1.0). Fewer operations (29% vs 21%, P =.02) and more repeat FNABs (3.9% vs 11%, P <.001) were performed in the BSRTC group. Sixty-one (16%) patients had A/FLUS, 56 with complete follow-up. Repeat FNAB in 26 patients was benign (11), A/FLUS (6), suspicious for malignancy (4), FN/HCN (2), and nondiagnostic (3). Thirty-two (57%) patients underwent thyroidectomy, and 6 patients (19%) were diagnosed with cancer. Conclusion: The BSRTC resulted in more frequent repeat FNAB, fewer thyroidectomies and no change in malignancy rate. In patients with A/FLUS, repeat FNAB was definitive in 65% with a rate of malignancy of 19%.