Fine-needle aspiration (FNA) cytology is a mainstay for the cytopathological diagnosis of thyroid nodules. FNA biopsy provides material for microscopic evaluation, but the collected specimens represent also an important source of material for ancillary studies. Cytological assessment of thyroid nodules is highly accurate, especially in categories where malignancy is confidently ruled out (TIR2) or ruled in (TIR4 and TIR5). In low-risk and intermediate-risk indeterminate nodules (TIR3A and TIR3B), the role of ancillary techniques in refining the risk of malignancy has been extensively studied. The use of immunocytochemistry and molecular diagnostics, especially in indeterminate categories, is progressively spreading throughout the scientific community. In some cases, molecular testing has been integrated in the diagnostic workup of thyroid cytology, and it influences clinical strategies.