Abstract: Thyroid nodule (TN) is a common endocrine disease in clinic, and the detection rate of ultrasound is ranging from 20% to 76%. It is of great significance to clarifythe pathological properties of TN for clinical selection of appropriate treatment. Ultrasound-guided fine-needle aspiration (US-FNA) is the gold standard for preoperative differential diagnosis of TN. The American Thyroid Association (ATA) recommends US-FNA for nodules with a diameter greater than 1 cm. Due to the limitations of US-FNA, the nature of US-FNA can not be clearly diagnosed in some samples, which brings difficulties to clinical treatment. Studies have shown that molecular testing for fine needle aspiration (FNA) samples can make up for the lack of cytopathological diagnosis to a certain extent. This article reviewed the progress of molecular markers in TN diagnosis and prognosis assessment.