Thyroid nodules present a serious problem, and mostly they do not carry neoplastic characteristics. Thus, they do not need to be surgically treated. The risk of malignancy varies from 5 to 15 %. Steps to diagnose malignancy should include a careful clinical evaluation, laboratory tests, a thyroid ultrasound exam and a fine-needle aspiration biopsy. Fine-needle aspiration biopsy (FNAB) is the most important diagnostic tool in the assessment of thyroid nodules. Today it is considered the gold standard for malignancy diagnosis in thyroid cancer. In this review we evaluate the role of FNAB and post-operative cytology in the evaluation of thyroid nodules. FNA results are classified as diagnostic (satisfactory) or nondiagnostic (unsatisfactory). Unsatisfactory smears (5–10 %) result from hypocellular specimens usually caused by cystic fluid, bloody smears, or suboptimal preparation. Diagnostic smears are conventionally subclassified into benign, indeterminate, or malignant categories. Benign cytology (60–70 %) is negative for malignancy, and includes cysts, colloid nodule, or Hashimoto thyroiditis. Malignant cytology (5 %) is almost always positive for malignancy, and includes primary thyroid tumors or nonthyroid metastatic cancers. Indeterminate or suspicious specimens (10–20 %) include atypical changes, Hurthle cells or follicular neoplasms. The new Bethesda Cytologic Classification has a 6-category classification, subdividing indeterminate further by risk factors. Considering the increasing worldwide incidence of thyroid microadenomas, recently it is recommended to undergo FNAB under ultrasound guidance even in small (< 1cm) nodules if they are correlated with suspicious ultrasonographic features or suspicious neck lymph nodes. FNAB is a cheap and reliable diagnostic tool that can be used in the selection candidates for surgery and pre-operative diagnosis of thyroid carcinomas. It was concluded that FNAB is the gold standard in the evaluation of thyroid nodules and can prevent many unnecessary surgeries. False-negative FNA cytology remains a concern for clinicians treating patients with thyroid nodules. Post-operative histology give the definitive diagnosis and studies confirm that it has a significant discordance between pre-operative cytology and post-operative histology in patients with thyroid nodule. Cytopathologists should strengthen their criteria for the identification of adenomatous hyperplasia, thyroiditis, cystic lesions or suspicious thyroid nodules to avoid misdiagnoses.