We report a case of multiple lymphoepithelial cysts of the thyroid gland in a patient with severe chronic lymphocytic thyroiditis. Lymphoepithelial cysts of the thyroid gland are rare lesions that are histologically similar to branchial cleft cysts found in the lateral neck. The cysts have an epithelial lining that is usually stratified squamous epithelium but may be focally respiratory-type epithelium. Abundant lymphoid tissue is present beneath the epithelium, and lymphoid follicles with reactive germinal centers are common features in the walls of the cysts. Because of their similarity to branchial cleft cysts and the presence of intrathyroidal branchiae-derived structures such as thymus and parathyroid gland tissue in the vicinity of some cysts, lymphoepithelial cysts of the thyroid have been postulated to arise from remnants of branchial derivatives; origination from solid cell nest remnants of the ultimobranchial bodies has been raised as a possibility. A definitive origin, however, has not been established. An association with chronic thyroiditis has been noted in 8 of the previously reported 16 cases occurring in a background of Hashimoto or chronic lymphocytic thyroiditis.