Purpose: Thyroid cancer is the most common endocrine cancer, developing in an average of 5%–7% of all nodules. In this study, we aimed to estimate the true risk, including multifocality and microcarcinomas, in patients who underwent total thyroidectomy after repeat Bethesda III cytology and in the other Bethesda groups. Methods: Three hundred patients participated in the study. Eighty-three (27.7%) of the patients were male and 217 (72.3%) were female. In the study, the diagnostic performances of the R-TIRADS (Revised Thyroid Imaging Reporting and Data System) classification used in the diagnosis of malignancy in thyroid nodules were compared with the Bethesda cytological classification. In order to compare the malignancy prediction powers, receiver operating characteristic curves were created for each system and area under the curve values were calculated. In all statistical analyses, a P-value below 0.05 was interpreted as statistically significant. A total of 150 cases (50.0%) with atypia of unknown significance (AUS) or follicular lesions of unknown significance (FLUS) were retrospectively evaluated. Results: Histopathology results were consistent with malignancy in 103 patients. Of these patients, 27 had multifocality (26.2%), 26 had microcarcinomas (25.2%), and 22 had both multifocality and microcarcinoma (21.3%). The majority of the carcinomas (46.6%) were seen to arise in AUS with cellular and nuclear atypias. Conclusion Prevalence of Bethesda category III cytologies is significantly higher than reported. A high rate of multifocality and incidental microcarcinomas in the definitive histopathology reports shows that the Bethesda classification falls short in the accuracy of risk in AUS/FLUS.