Published data suggest that the Bethesda System for Reporting Thyroid Cytopathology (BSRTC) is valuable in directing therapy of thyroid nodules. Literature examining the effect of the BSRTC on management when compared with pre BSRTC is lacking, however. This study evaluates the impact of applying the BSRTC retrospectively to a series of patients who underwent surgery after a fine-needle aspiration biopsy (FNAB) classified using the pre BSRTC system, and investigates how the BSRTC application to the same population would have ultimately affected the management strategy. One hundred patients who had previously undergone both FNAB and thyroidectomy before implementation of the BSRTC were randomly selected. Each FNAB was examined by a single cytopathologist (blinded to both the original interpretation and the surgical pathology findings) and reclassified using the BSRTC. Accuracy of both systems was examined using the final pathology as the true diagnosis. Of 68 FNABs initially classified as indeterminate, 32 (47.1%) were reclassified as benign. There was no significant difference in overall rates of detection of malignancy on final pathology in specimens classified as benign, both pre and post application of the BSRTC (P = 0.70). Application of the BSRTC resulted in a significant percentage of indeterminate specimens being reclassified as benign, presumably due to more standardized criteria for interpretation and reporting. No significant change in detection of malignancy was observed. We conclude that application of the BSRTC may result in lower rates of thyroidectomy, while preserving the same diagnostic accuracy in the detection of thyroid malignancy.