Background: The Bethesda classification system for reporting on thyroid fine-needle aspiration (FNA) cytology was recently proposed by the National Cancer Institute, USA. We aimed to report our experience with applying this system for thyroid FNA, with a focus on comparing it with the four categorical system. Methods: We retrospectively reviewed the 4,966 thyroid FNAs that were performed at the Seoul St. Mary's Hospital between October 2008 and September 2009. All the FNAs were classified according to the Bethesda system and the four tier system. Results: The cytologic diagnoses of the Bethesda system included 10.0% unsatisfactory, 67.7% benign, 3.1% atypia of undetermined significance, 0.6% follicular neoplasm, 0.5% follicular neoplasm, Hürthle cell type, 5.1% suspicious for malignancy and 13.0% malignancy. Using four tier system, 10.1%, 67.6%, 9.3%, and 13% were diagnosed as unsatisfactory, negative for malignancy, atypical cells and malignancy, respectively. Of the 4,966 nodules, 905 were histologically confirmed. The specificity of the Bethesda system and the four tier system for diagnosing malignancy was 99.6% and 82.6%, respectively. Conclusions: The Bethesda system can classify indeterminate thyroid nodules into more detailed categories and provide clinicians with useful information for management.