In conclusion, our study shows that SOX2 and BMI1, two cancer cell stemness-related genes, are regulated by the Shh pathway in thyroid cancer; Gli1 expression correlates with the levels of SOX2 and BMI1 in the PTC specimens; Inhibition of the Shh pathway leads to the retardation of thyroid CSC-driven tumor growth but does not significantly affect the growth of tumor xenografts derived from bulk thyroid tumor cells; ALDH-positive thyroid CSCs express high levels of the SOX2 and BMI genes and are highly tumorigenic. Here, SOX2 is linked to thyroiditis.