BackgroundThe involvement of granulomatosis with polyangiitis is less frequent in the intestine.Case presentationWe present a case of Wegener’s granulomatosis with unusual endoscopic appearance, involvement in a young man’s gastrointestinal tract. A 45-year-old man was diagnosed with Wegener’s granulomatosis 11 years ago, and relapsed with abdominal pain and melena. A colonoscopy was performed, and the appearance of mucosal lesions with an unusual annular black membrane was observed. A black ring-shaped membranous tissue adhered to the surface of the colon wall, which could be traversed by an endoscopic forepart.ConclusionBiopsy of the black membrane revealed degenerative colonic mucosal tissues, while deep colonic biopsy revealed inflammatory granulation tissues. This has not been reported in previous documents.