Background Fine-needle aspiration cytology (FNAC) has become a well-established modality in the diagnosis, staging and follow-up of thyroid nodules. FNAC outcomes are routinely classified using the Bethesda System for Reporting Thyroid Cytopathology (BSRTC), facilitating appropriate clinical management. Bethesda categories III and IV encompass varying risks of malignancy. This retrospective study established a possible association between these cytological categories and malignancy rates in patients treated at a single institution. Methods Over a 6-year period, 11,627 FNAC procedures were performed on thyroid nodules. Of these, 814 (59.63%) patients were submitted to thyroidectomy. The nodules of 108 patients were classified as Bethesda category III and 47 patients as Bethesda category IV. Patient data were reviewed to establish a correlation between the FNAC results and the final histopathological analyses. Results The rates of malignancy among patients who underwent surgery were 25% for category III and 27.6% for category IV, with no significant differences between categories (p = 0.67). The pathological parameters of malignant nodules, namely tumour type, size, encapsulation, invasion into the thyroid capsule, extrathyroidal extension and lymphovascular invasion did not significantly differ between the groups (p > 0.05). Conclusions This paper provides a more precise correlation of malignancy rates with thyroid nodules classified as Bethesda categories III and IV, as our findings are comparable to the literature, giving malignancy rates ranging from 10 to 30% for category III and 25-40% for category IV. Use of the BSRTC is heterogeneous across institutions, and there is some degree of subjectivity in the distinction between categories III and IV; therefore, it is crucial to estimate the rates of malignancy at each institution. Molecular assays are of increasing importance in determining the need for surgical intervention for thyroid lesions. Gene expression assays using FNAC material may demonstrate a high predictive value for cytologically indeterminate thyroid nodules diagnosed as Bethesda classes III and IV.