Every year in Italy, about 60,000 new cases of nodular thyroid pathology are diagnosed, of which almost 30% are cytologically indeterminate (TIR3A/3B). The risk of malignancy reported in the literature on thyroid nodules ranges from 5% to 15% for TIR3A and from 15% to 30% for TIR3B. It is suspected that these percentages are higher in practice. We performed univariate and multivariate analyses of clinical risk factors. The medical records of 291 patients who underwent surgery for cytologically indeterminate nodular thyroid disease were retrospectively reviewed. Clinical parameters and preoperative serum markers were then compared between the benign nodular thyroid disease and thyroid cancer groups. For each patient, clinical characteristics, comorbidities, neck ultrasonographic features, and histological reports were statistically analyzed using Chi-squared and Fisher's exact tests. A total of 134 malignant neoplasms were found (46%), divided into 55 cases (35%) in the TIR3A group and 79 cases (59%) in the TIR3B group. Statistical analysis was not significant in both populations for both sex and age (TIR3A p-value = 0.5097 and p-value = 0.1430, TIR3B p-value = 0.5191 p-value = 0.3384), while it was statistically significant in patients with TIR3A nodules associated with thyroiditis (p-value = 0.0009). In addition, the patients with TIR3A and 3B nodules were stratified by ultrasound risk for the prediction of malignancy and it was significant (p = 0.0004 and p < 0.0001). In light of these results, it emerges that surgical treatment of nodular thyroid pathology with indeterminate cytology TIR3A should always be considered, and surgery for TIR3B is mandatory.