In this study, our aim was to test the usefulness of The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) in indeterminate lesions in which cytological and histological diagnosis discordance was high and to investigate the contribution of TBSRTC in this indeterminate diagnostic group. The medical records of the patients who presented to the Haydarpasa Numune Training and Research Hospital in Istanbul, Turkey, between October of 1999 and September of 2010, for the cytological and histological diagnosis of thyroid nodules, were reviewed retrospectively. We reclassified these patients according to the Bethesda method, which features well-defined cytological criteria for each category within a six-tiered system. For each patient, the diagnosis and reasons for discordance were discussed and a final decision was made for each discordant case. The overall distribution of the cytological diagnoses using an in-house system was as follows: 811 benign (73.7 %), 87 suspicious follicular cell/follicular neoplasia (7.9 %), 52 suspicious for malignancy (4.7 %), and 45 malignant (4.1 %). We reclassified the diagnoses using the Bethesda system and the results are as follows: 797 benign (73.7 %), 48 follicular lesion of undetermined significance (4.3 %), 68 follicular neoplasia (7.9 %), 40 suspicious for malignancy (3.6 %), and 44 malignant (4 %). Our results showed that using TBRSTC for the lesions in the indeterminate category decreased the ratios of false-positive and falsenegative diagnoses.