Wegener's granulomatosis (WG) is an autoimmune disorder characterized by the involvement of many organ systems. In patients with refractory disease, the efficacy of cyclophosphomide, corticosteroids and infliximab has been reported recently. Even in cases with serological response, disease progression has still been observed. Herein, we report a case of WG, most likely accompanied with subacute granulomatous thyroiditis while the patient was on cyclophosphamide, corticosteroid and infliximab therapy. As for as we know, this is the first time that such a copresentation has been observed, suggesting that mechanisms other than T-cell-mediated cytotoxicity may be important in the pathogenesis of granulomatous thyroiditis.