Thyroid fine-needle aspiration (FNA) cytology is a fast growing field. One of the most developing areas is represented by molecular tests applied to cytological material. Patients that could benefit the most from these tests are those that have been diagnosed as “indeterminate” on FNA. They could be better stratified in terms of malignancy risk and thus oriented with more confidence to the appropriate management. Taking in consideration this need to improve and keep high the yield of thyroid FNA, professionals from various fields (i.e. molecular biologists, endocrinologists, nuclear medicine physicians and radiologists) are refining and fine-tuning their diagnostic instruments. In particular, all these developments aim at increasing the negative predictive value of FNA to improve the selection of patients for diagnostic surgery. These advances involve terminology, the application of next-generation sequencing (NGS) to thyroid FNA, the use of immunocyto- and histochemistry, the development of new sampling techniques and the increasing use of nuclear medicine as well as molecular imaging in the management of patient with a thyroid nodule. Herein, we review the recent advances in thyroid FNA cytology that could be of interest for the “thyroid-care” community, with particular focus on the indeterminate diagnostic category.