Two cases of intrathyroidal lymphoepithelial cyst are described. Both of them were solitary, one being found incidentally in a patient operated on for a multinodular goiter, the other being clinically obvious as a cold nodule. They exhibited features of cysts of branchial cleft origin, i.e. squamous cell lining epithelium and abundant lymphoid tissue with reactive germinal centers. The thyroid gland parenchyma showed a discrete lymphoid infiltration consistent with the diagnosis of focal lymphocytic thyroiditis. In the first case a single epidermoid solid cell nest was found. The histogenesis of intrathyroidal lymphoepithelial cysts remains unclear, but their origin from cystically degenerated ultimobranchial body remnants (solid cell nests) seems to be most probable. This assumption is supported by a similar immunohistochemical profile of solid cell nests and epithelial cells lining the cysts and also by the presence of one solid cell nest in the proximity to the cyst in one of our cases.