Fine needle aspiration (FNA) is accepted as the diagnostic procedure of choice in the management of patients with thyroid nodules. Follicular/Hürthle cell neoplasms have traditionally been grouped under the category of indeterminate FNA results. This study examined the experience with FNA in a large cohort of patients undergoing thyroidectomy before adoption of the Bethesda system for reporting thyroid cytopathology (BSTC) at a single academic medical center. A retrospective review of prospectively collected data of 797 consecutive patients with dominant nodules >1 cm who underwent FNA and thyroidectomy from 2003 to 2009 was performed. Patients were categorized into groups based on FNA results: malignant, benign, indeterminate, and nondiagnostic. The indeterminate group had FNA results that included follicular neoplasm, Hürthle cell neoplasm, and suspicion of papillary thyroid cancer. FNA results were compared with final histopathology after thyroidectomy. FNA results included 147 (18%) positive for malignancy, 255 (32%) benign, 358 (45%) indeterminate, and 37 (5%) nondiagnostic. The overall malignancy rate on final histopathology was 369 of 797 (46%). Overall, there was a false positive rate of 2% and false negative rate of 8.6%. Among the 358 indeterminate FNA results, carcinoma was found in 81 (36%) of 223 follicular neoplasms, 18 (36%) of 50 Hürthle cell neoplasms, and 78 (92%) of 85 that were suspicious for papillary thyroid cancer. When FNA was nondiagnostic, cancer was present in 9 of 37 (24%). Among 39 patients with benign FNA who had cancer on final histopathology, 22 of 255 (8.6%) had cancer in the index thyroid nodule, and 81% of cancers were >1 cm. Patients with FNA and dominant nodules >1 cm, who underwent thyroidectomy, had an overall rate of thyroid malignancy of 46%. There was a cancer prevalence of 8.6% in patients with benign FNA results referred for surgical resection. Despite not yet implementing the BSTC at this medical center, the majority of thyroidectomies were adequately performed for indeterminate FNAs with underlying malignancy.