Homeodomain, forkhead domain, and paired domain-containing transcription factors play a major role in development, tissue-specific gene expression, and tissue homeostasis in organs where they are expressed. Recently, their roles in stem cell and cancer biology are emerging. In the thyroid, NKX2-1, FOXE1, and PAX8 transcription factors are responsible for thyroid organogenesis and expression of thyroid-specific genes critical for thyroid hormone synthesis. In contrast to their known roles in gene regulation, thyroid development and homeostasis, their involvement in stem cell, and/or cancer biology are still elusive. In order to further understand the nature of thyroid cancer, it is critical to determine their roles in thyroid cancer.