A case of Wegener granulomatosis as a cause for fever of unknown origin (FUO) and secondary involvement of endocardium in association with mitral valve prosthesis is presented. Although the patient was referred as a case of unresolving pneumonia, her unresponsiveness to broad spectrum antibiotics including infective endocarditis treatment prompted investigation for a non-infectious aetiology for her FUO, leading to a diagnosis of Wegener granulomatosis.