Thyroid nodules are quite common and present approximately in 10% of the population. Fine-needle aspiration biopsy has become the mainstay of thyroid nodule evaluation and the overall accuracy is excellent; however, some aspirates demonstrating indeterminate cytology results do not permit definitive diagnosis of malignancy, and in addition, there are no clear guidelines for the management of these lesions because the incidence of malignancy in indeterminate aspirates varies in the different studies published. In order to find molecular markers in an attempt to predict malignancy based on cytology, at least 70 molecular or cellular and genetic markers have been studied in thyroid nodules. This review focuses on some potential markers such as thyroid peroxidase, thyroglobulin, telomerase, galectin-3, RET/PTC and protein p53; some of them, such as thyroid peroxidases, thyroglobulin and galectin-3, can be studied in a routine pathology laboratory and are promising, but do not yet fulfil criteria required for their use in clinical practice. The American guidelines and the European consensus for the management of thyroid nodules and differentiated thyroid cancer do not recommend their systematic use because the evidence that they have provided is insufficient. On the other hand, information obtained through cytological smears permits the study of complex metabolic or genetic pathways, providing researchers with a high throughput tool to elucidate changes in the global expression patterns seen in tumour cells. This ability to take tumour biology into account would allow the selection of different drugs, considering the predominant altered pathways observed in these samples. Finally, all these data may provide the molecular groundwork for permitting future preoperative discrimination of follicular adenomas from hyperplastic nodules, and may ultimately guide therapeutic strategies.