Several oncogenes are involved in the development of thyroid cancer. In the last 10 years, different techniques have been applied to study point mutations and genetic rearrangements. Some of them have been used only on thyroid specimens and need to be tested on FNAC material. Generally, these modifications can be studied by various PCR-based techniques, and results depend on the quality and quantity of the starting material. By carefully selecting the appropriate methods, researchers have demonstrated that the detection of genetic alterations is feasible in a FNAC samples. This may refine the diagnosis of thyroid cancer, especially for those samples which are deemed cytologically inadequate.