A 19-year-old man with known Hunter syndrome presented with dyspnea, and was admitted to our hospital. Bronchoscopy revealed tracheal narrowing with excessive granulation tissue formation in the trachea. Three-dimensional CT clearly demonstrated severe stenosis in the trachea and both main bronchi. Autopsy showed granulomatous tissue proliferation and deposition of mucopolysaccharide in the tracheal wall. We demonstrated the clinico-radiological-pathological correlation of bronchial lesions in Hunter syndrome, and emphasized that three-dimensional CT is helpful in deciding upon therapeutic strategy to treat stenosis in the large airway.