Cardiac involvement in Wegener granulomatosis is uncommon. We report a case of Wegener granulomatosis that presented as culture-negative endocarditis with aortic valvular vegetation. The clinical manifestations included gingival hyperplasia, gangrenous digital infarcts, mononeuritis multiplex, high fever, inflammatory arthritis, pansinusitis, splenic infarct, and aortic valvular vegetation, which underscore the difficulty of distinguishing systemic vasculitis from bacterial endocarditis. Contrary to the common notion that valvular vegetation is invariably associated with bacterial endocarditis, this case proves that such findings can occur in Wegener granulomatosis as well. Clinicians are guided toward early treatment with corticosteroids and cyclophosphamide to prevent fatal complications.