Various approaches are available for the management of nodules that are evaluated to be indeterminate according to the results of thyroid fine needle aspiration biopsy. The present study aimed to determine the rate of malignancy and the ultrasonographic features that could be used as predictor of malignant pathologies at the nodules with indeterminate cytology. A total of 201 patients who underwent total thyroidectomy and whose fine needle aspiration biopsy results were evaluated to be Hurthle cell lesion (n = 99), follicular neoplasm (n = 61) and [corrected] suspicious for malignancy (n = 41) were enrolled in this study. Of these patients, 178 were females (88.6 %) and 23 were males (11.4 %). The rates of malignancy were found to be 33.3 % in the Hurthle cell lesion group, 23.0 % in the follicular neoplasm group and 53.7 % in the suspicious for malignancy group (p = 0.006). The comparison of the ultrasonographic characteristics of the malignant and benign nodules revealed hypoechogenicity and microcalcification to be more common in malignant nodules (34.3 vs. 16.9 %, p = 0.005; 27.1 vs. 13.1 %, p = 0.014; respectively). While 92.3 % of the malignant nodules were ≥1 cm, 82.9 % of the benign nodules were ≥1 cm (p = 0.042). We believe that as the patients at Hurthle cell lesion group have higher risk of malignancy than the patients with Follicular Neoplasia so total thyroidectomy will be suitable for these patients. [corrected]. In addition, microcalcification and hypoechoic nodules at patients with indeterminate cytology can be related with increased risk of malignancy. [corrected].