Objective: To evaluate the effectiveness of the Bethesda System for Reporting Thyroid Cytopathology (BSRTC) and to analyze the causes of unclear diagnoses following BSRTC adoption. Study Design: According to the BSRTC, we reclassified cytologic samples originally diagnosed as ‘indeterminate’ with sequential surgical resection. Then, we analyzed the causes of cases, which were recategorized as ‘atypia undetermined significance/follicular lesion of undetermined significance (AUS/FLUS)’. Results: According to the BSRTC, 154 ‘indeterminate’ cases were reclassified as follows: unsatisfactory, n = 5 (3.2%); benign, n = 43 (27.9%); AUS/FLUS, n = 77 (50.0%); suspicious for a follicular neoplasm, n = 7 (7.1%); suspicious for a Hürthle cell neoplasm, n = 4 (2.6%); suspicious for malignancy, n = 15 (9.7%), and malignancy, n = 3 (1.9%). Then, the AUS/FLUS group was analyzed according to the scenarios proposed by the BSRTC. Fifty-nine (58.9%) cases of AUS/FLUS were due to suboptimal preparation. In addition, papillary microcarcinoma and coexisting Hashimoto’s thyroiditis caused inconclusive diagnoses. Conclusion: The BSRTC can be easily applied to thyroid fine-needle aspiration. We were able to reclassify indeterminate thyroid nodules into more detailed categories and thus reduce the number of cases classified as indeterminate. However, suboptimal preparation, papillary microcarcinoma, and coexisting Hashimoto’s thyroiditis precluded cytopathologists from making definitive diagnoses.