Ultrasound-guided fine-needle aspiration (FNA) is the most valuable procedure in the diagnosis of thyroid nodules. One possible result of FNA of thyroid nodules, however, is "nondiagnostic" cytology. In these cases, consensus guidelines suggest repeating FNA with ultrasound guidance, but the results obtained may continue to be nondiagnostic. These results cause confusion due to the fact that there exist conflicting potential treatment modalities, such as performing diagnostic surgery or recommending follow-up. Hence, the present study aimed to establish a protocol for performing diagnostic operations for thyroid nodules with repeat nondiagnostic cytology. This study was performed on patients who underwent ultrasound-guided FNA and molecular testing for BRAF gene mutation. Out of 1,203 patients, 84 had nondiagnostic cytology and were BRAF negative, and ultrasound-guided FNA was repeated on these patients. Out of this group, 54 patients once again had nondiagnostic cytology, and 51 of these underwent diagnostic surgery. We analyzed the characteristics and ultrasonographic findings of the group of patients with repeat nondiagnostic cytology. On the initial ultrasound-guided FNA, the percentage of patients with nondiagnostic cytology was 6.98 %, and on repeat ultrasound-guided FNA, the percentage of patients with nondiagnostic cytology was 67.5 %. The majority of these patients underwent diagnostic surgery, and 36 (70.6 %) patients were diagnosed as having a malignant thyroid nodule, while15 (29.4 %) patients were diagnosed with a benign nodule. Univariate analysis showed a significant difference in the size of the nodule, hypoechogenicity, and microcalcification in the ultrasonography findings. Multivariate analysis revealed only hypoechogenicity as a factor that showed a significant difference (p value 0.017, 95 % confidence interval 1.494-62.426).The diagnostic accuracy of the ultrasonography was 76.5 %. Hypoechogenicity on ultrasonography represents an excellent parameter for the selection of those who should be referred for diagnostic operation among patients with thyroid nodules and repeat nondiagnostic cytology.