Class II transactivator (CIITA) is the master regulator of MHC class II genes, and mediates their induction by interferon gamma (IFN gamma). To study the role of CIITA in modulating the expression of thyroid-specific genes, we cloned the full-length rat CIITA and use it to transfect a rat thyroid cell line. We found that only one type of CIITA, type TV, is induced in thyroid cells upon IFN gamma stimulation, and that CIITA is capable not only of inducing the expression of MHC genes in the thyroid, but also of differentially suppressing the expression of thyroid-specific genes. These findings suggest new avenues for the development of thyroid autoimmune diseases.