Palpable thyroid nodules are a common clinical entity found in 4 % to 7 % of the general population. Ultrasonography and fine-needle aspiration (FNA) cytology are worldwide accepted methods to discriminate between benign and malignant lesions. Nevertheless, 10-30 % of the biopsied nodules exhibit “indeterminate ” cytology. The objective of the new reporting systems is to encourage further investigation of these nodules and to lower the overall incidence of false-negative FNA results. In particular, molecular testing for a panel of somatic mutations is feasible using thyroid FNA material and has been revealed as a powerful adjunct to visual microscopic evaluation, since 60-70% of the thyroid cancers harbor at least one known genetic alteration. A sensitive preoperative test that would allow safe identification of clearly benign nodules with indeterminate cytology raises the prospect of avoiding a purely diagnostic surgery. Here, we reviewed the more recent knowledge of gene expression profiling in cytologically indeterminate thyroid nodules and we reported our experience on nCounter Analysis System from NanoString Technologies.