cDNA encoding 287 amino acids of the C-terminus of mouse thyroglobulin was cloned and sequenced. The amino acid homology between mouse and rat thyroglobulin was 96%, and was 78% between mouse and human. It was found that mouse thyroglobulin completely shared homology with two thyroiditogenic peptides described by other investigators. These findings are consistent with our hypothesis that in murine experimental thyroiditis, the primary thyroiditogenic epitopes are encoded by mouse-specific regions of thyroglobulin.