Recent genetic studies have identified germline allelic variation in and near FOXE1 to be strongly associated with non-medullary thyroid cancer risk including single nucleotide variants rs965513[A] (56 kb upstream of FOXE1) [13–18] and rs1867277[A] (within its promoter) [19–21], and variation within the FOXE1 polyalanine tract [22–24]; resolution of causal variants responsible for the association with thyroid cancer has been difficult due to strong linkage disequilibrium between all three variants. Here, FOXE1 is linked to thyroid cancer.