Introduction: The thyroid gland is arguably the fastest growing anatomic site for fine needle aspiration (FNA). With the increase of thyroid cases, a reevaluation of cytotechnologist screening quality metrics in terms of thyroid FNA is called for. We present our institutional cytotechnologist performance at screening for nuclear atypia by applying established quality metrics. Materials and Methods: Information on 8,814 consecutive thyroid cytopathology cases over a 10-year period was retrieved from computerized records. A subsample of cases categorized either as atypia of uncertain significance with nuclear atypia or suspicious for malignancy with features suspicious for papillary thyroid carcinoma. The cytotechnologist and cytopathologist diagnoses were compared using step discrepancies and Δ-ratios. Results: Overall discrepancy between the cytotechnologist and cytopathologist diagnoses existed in <10% of all thyroid cases. One-category discrepancies were the most common (7.8%), while two-category discrepancies were rare (0.5%). The one-category discrepancy rate correlated with cytotechnologist experience. One-category undercalls were twice as common as overcalls (5.3 vs. 2.5%, p < 0.0001). Conclusions: We identified a high level of quality in the screening for nuclear atypia in thyroid FNA. The one-category discrepancy rate is suited to tracking individual cytotechnologist performance, identifies outliers and appears to correlate with cytotechnologist experience.