Early diagnosis is crucial for effective treatment of Wegener's granulomatosis, although this disease shows only atypical symptoms in the primary stage. This report describes a patient suspected of having a malignancy based on integrated 18F-fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT), which showed increased uptake in pulmonary nodules and nasopharyngeal mucosa. Integrated PET/CT is therefore considered to be useful to confirm the distribution and determine the optimal site for biopsy.