A 54-year old Wegener's granulomatosis patient with PR3-ANCA at diagnosis 2 years ago was admitted with a pulmonary relapse and new subglottic stenosis preceded by pulmonary infections. The patient presented with bactericidal/permeability increasing protein (BPI)-ANCA in ELISA whereas at the same time PR3-ANCA had disappeared. Bronchoalveolar lavage revealed pulmonary infection with Gram-negative bacteria. After antibiotic treatment, immunosuppression was started with cyclophosphamide and infliximab due to refractory disease. Remission was induced and BPI-ANCA disappeared. A bacterial growth inhibition assay with BPI and the patient's IgG purified during the actual pulmonary relapse showed inhibition of the antimicrobial activity of BPI in vitro, in contrast to IgG from sera taken 2 years before and after remission was induced. The patient's BPI-ANCA recognised the bioactive N-terminal portion of BPI. Thus a possible mechanism is demonstrated for how BPI-ANCA may contribute to a pro-inflammatory setting during the development of a pulmonary relapse in the absence of PR3-ANCA by impeding bacterial clearance.