Wegener’s granulomatosis (WG) is a systemic vasculitis characterised by the presence of necrotizing granulomas and classically manifests as a triad of upper and lower respiratory tract involvement along with glomerulonephritis. Other rather unusual presentations of WG include ocular, salivary gland, cutaneous, gastrointestinal and cardiac involvement. We report a case in a 51-year-old woman suffering from WG with positive antineutrophil cytoplasmic autoantibodies and antibodies directed against proteinase 3. Under maintenance therapy, the patient developed two thyroid nodules suspicious for malignancy which led to thyroidectomy. Postoperative histological examination revealed a tumour-forming WG mimicking a malignant thyroid tumour. We conclude that, although extremely rare, Wegener’s granulomatosis should be added to the list of differential diagnoses of tumours of the thyroid gland.