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Background The involvement of granulomatosis with polyangiitis is less frequent in the intestine. Case presentation We 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,...