Fine needle aspiration cytology informs the surgeon on surgical management of thyroid nodules. Approximately 70% of thyroid nodules are benign by cytology and can largely be observed. Surgery is required for the 10 ~ 15% of nodules that are suspicious for malignancy or malignant. Approximately 20 ~25% of thyroid nodules are cytologically indeterminate and 75 ~ 80% of these cytologically indeterminate nodules are benign on final pathology. This leads to the problem of 2-stage operations for nodules that are also indeterminate on frozen section, that are malignant; and unnecessary surgery for many cytologically indeterminate thyroid nodules that are benign. Molecular testing for indeterminate thyroid nodules improves specificity analysis and positive predictive value (PPV). Molecular alteration testing can reduce the number of completion thyroidectomies with mutations specific for papillary thyroid cancer (PTC). Indications favoring "rule in" testing include Bethesda grade 3 and 4 indeterminate thyroid nodules, with a high institutional prevalence of cancer, high risk ultrasound features, a highly specific mutation for cancer, and a surgeon favoring total thyroidectomy for differentiated thyroid cancer (DTC) < 4 cm. The negative predictive value (NPV) of a cytologically benign nodule is 96.3% and this is equivalent to the NPV of several molecular panels. Molecular testing for indeterminate thyroid nodules improves sensitivity analysis and NPV. Surgery can be avoided in selected cases with molecular tests. There is limited testing against a true gold standard, since benign nodules as determined by molecular tests rarely undergo definitive histologic evaluation; thus active surveillance is necessary.