© 2016 John Wiley & Sons Ltd.Background: A fine needle aspiration biopsy (FNAB) is the most valuable diagnostic procedure for preoperative discrimination of benign and malignant nodules. The Bethesda System for Reporting Thyroid Cytopathology provides standardised reporting and cytomorphological criteria in aspiration smears. The aim of the present study was to determine malignancy rates in nodules with different cytology results and evaluate the diagnostic value of Bethesda for variants of papillary thyroid carcinoma (PTC). Materials and methods: A retrospective analysis of 2534 cases with 5784 thyroid nodules, who underwent FNAB followed by surgery, were included in this study. FNAB was performed with ultrasonography guidance. Cytological diagnoses were classified as: non-diagnostic (ND), benign, atypia of undetermined significance/follicular lesions of undetermined significance (AUS/FLUS), follicular neoplasm/suspicious for follicular neoplasm (FN/SFN), suspicious for malignancy (SUS) and malignant. Histopathological diagnoses were classified into four groups: benign, PTC, follicular thyroid cancer and other types of thyroid cancer (including medullary thyroid cancer, undifferentiated thyroid cancer and thyroid tumours of uncertain malignant potential). Cases with PTC were further divided into four categories: conventional variant, follicular variant, aggressive variants (tall cell, diffuse sclerosing and columnar variant) and other variants (oncocytic, solid/trabecular and warthinlike variants). FNAB results were compared with histopathological results. Results: Malignancy rates were 6.3%, 3.2%, 20.7%, 33.3%, 74.2% and 95.6% in the nodules with ND, benign, AUS/FLUS, FN/SFN, SUS and malignant cytology results, respectively. Pre-operative cytology was malignant or SUS in 56.6% of conventional, 24.3% of follicular, 92% of aggressive and 41.7% of other variants of histopathologically confirmed PTC. The difference between the groups was significant (P < 0.001). Conclusion: The Bethesda classification is a reliable indicator of malignancy in nodules with different cytology results and seems to be very effective in predicting the malignancy for the nodules diagnosed with aggressive variant PTC on the final histological examination.