Alpha-1-antitripsyn neutralizes the tissue damaging effects of proteases. Alpha-1-antitripsyn deficiency manifests with necrotizing vasculitis. Wegener's granulomatosis is a systemic necrotizing vasculitis that uncommonly affects the gut. The molecular genetics of patients with Wegener's granulomatosis of the gastrointestinal tract have never been characterized. A 63-year-old man with emphysema was admitted with a fever of unknown origin. Initially, this fever was linked to ileocolic Crohn's disease and later attributed to antineutrophil cytoplasm antibody-positive systemic vasculitis. Genetic analysis revealed that the alpha-1-antitripsyn deficiency was due to a previously unreported compound heterozygosity for two mutations (PiZ and PiMProcida). Our findings appear to support the concept that severe alpha-1-antitripsyn deficiency is implicated in the pathogenesis of the Crohn's disease-like milder intestinal manifestations belonging to the spectrum of Wegener's granulomatosis.