Thyroid nodule (TN) is a common endocrine disease. The treatments and prognoses can be very different due to the malignant and benign property of the TN. Malignant TN lacks characteristic signs or symptoms, and the accuracy of ordinary diagnostic methods is not very satisfactory. Fine-needle aspiration (FNA) can improve the accuracy by obtaining a small amount of suspected thyroid cells for cytological diagnosis. The paper is to review the achievements made in FNA and the related molecular biology for the diagnosis of TN in recent years.