Background:Fine needle aspiration (FNA) cytology is a popular, reliable and cost effective technique for the diagnosis of thyroid lesions. The aim of our study was to review cases of misclassified primary malignant neoplasms of the thyroid by FNA, and assess the causes of cytologic misdiagnosis and their impact on clinical management.Methods:Clinical data, FNA smears and follow-up surgical specimens of cases diagnosed with primary thyroid carcinoma were reviewed.Results:Of the 365 cases with a malignant diagnosis by FNA over a period of 11 years, nine (2.4 %) were identified with discrepant histologic diagnosis with regard to the type of primary thyroid malignancy. In addition, four cases were added from the consultation files of the Massachusetts General Hospital. Areas of difficulty contributing to misclassification included overlapping cytologic features (n = 6), rarity of tumors (n = 3), and sampling limitations (n = 4). Of the 13 cases, 12 underwent total or near total thyroidectomy and one patient had concurrent surgical biopsy. Measurement of serum calcitonin levels in one case, with an initial cytologic diagnosis of medullary carcinoma, prevented unnecessary lymph node dissection. Misclassification of medullary carcinoma as papillary carcinoma precluded lymph node dissection in one case. Further management decisions were based on the final histologic diagnosis and did not require additional surgery. Two cases of undifferentiated (anaplastic) thyroid carcinoma were misdiagnosed as papillary thyroid carcinoma. Both patients received total thyroidectomies, which may not otherwise have been performed.Conclusions:A small subset of primary malignant neoplasms of the thyroid may be misclassified with regard to the type of malignancy on FNA. The majority of primary malignant neoplasms diagnosed on FNA require thyroidectomy. However, initial cytologic misclassification of medullary carcinoma or undifferentiated carcinoma as other malignant neoplasms or vice versa may have an impact on clinical management.