Fine needle aspiration cytology (FNAC) of thyroid nodules is the best screening test for the selection of patients that may require surgical management. However, the diagnosis of follicular neoplasm on FNAC remains a gray area and the main differential diagnosis of follicular neoplasm includes benign (nodular hyperplasia and follicular adenoma) and malignant (follicular carcinoma and follicular variant of papillary carcinoma) lesions. The cytologic diagnosis of follicular neoplasm is based on the high cellularity, microfollicular or trabecular pattern, overlapping follicular cells, and scanty or absent colloid. Histologically, the diagnosis of follicular carcinoma requires the presence of tumor capsular invasion or vascular invasion. In the follicular variant of papillary carcinoma, nuclear features of papillary carcinoma may be subtle and seen in only a small number of cells, and thus may not be readily appreciated. Analyses of BRAF and RAS point mutations and RET/PTC and PAX8/PPARγ rearrangements have been reported to be a useful ancillary tool for diagnosing thyroid cancer in cytology specimens. The presence of BRAF or RET/PTC mutation is a strong indicator of papillary carcinoma. PAX8/PPARγ rearrangement is exclusively found in follicular carcinoma. RAS mutations are found in follicular adenoma/carcinoma and follicular variant of papillary carcinoma. Therefore, molecular testing of FNAC samples can improve the accuracy of cytologic diagnosis.