The incidence of thyroid cancer, which encompasses various clinical and histological entities, has increased significantly during the past few decades. The majority (95%) of thyroid malignancies are follicular cell-derived thyroid cancers, including papillary thyroid carcinoma, follicular thyroid carcinoma, poorly differentiated thyroid carcinoma, and undifferentiated (anaplastic) thyroid carcinoma. With the publication of genomic studies, the understanding of the molecular landscape of follicular cell-derived thyroid cancers has vastly improved, opening up promising new therapeutic targets. In this review, the molecular alterations will be described along with the effects of molecular markers on the monitoring and management of thyroid cancers.