Wegener's granulomatosis is a disease characterized by a necrotizing vasculitis and granulomatous inflammation. The localized form involves the upper and/or lower respiratory tracts while in the common generalized form there is a widespread necrotizing vasculitis and renal involvement. Although gastrointestinal involvement which has been detected at necropsy in 24% of the cases is an uncommon finding, it might cause severe complications. We report a patient with clinical Wegener’s granulomatosis who subsequently developed gastrointestinal perforation. Gastrointestinal perforation was treated with surgical resection and the patient survived under the treatment of cyclophosphamide and prednisolone with no further gastrointestinal complications. The present case indicates that the gastrointestinal complications might be considered in natural history of Wegener’s granulomatosis.