Autoimmune polyglandular syndromes are rare disorders characterized by failure of several endocrine glands, as well as non-endocrine organs, associated with immune-mediated tissue destruction. We report a rare case of polyglandular syndrome type II in a patient who presented with premature ovarian failure, Hashimoto’s thyroiditis and empty sella associated with a diagnosis of differentiated thyroid carcinoma. This case probably represents the first report on this tumor in a patient with polyglandular disorder.