A 43-year-old woman, with a 3-month history of fatigue, anaemia and swollen lymph nodes, underwent biopsy of a lymph node, which revealed reactive lymphadenopathy. Due to an increased serum creatinine concentration and severe proteinuria, a kidney biopsy was performed, which revealed diffuse, segmental, proliferative, immune-complex glomerulonephritis with crescents. Electron microscopy showed tubulo-reticular structures within one endothelial cell. These were a typical clinical presentation and compatible histopathological findings for systemic lupus erythematosus; however, the anti-myeloperoxidase antineutrophil cytoplasmic antibody (MPO-ANCA) level was extraordinarily high. In spite of treatment with intravenous cyclophosphamide and methylprednisolone pulse therapy, the patient's kidney function declined. Starting plasma exchange improved her renal function and removed MPO-ANCAs, which were suspected to play the major role in the pathogenesis of glomerulonephritis. These findings indicate that in addition to lupus nephritis, MPO-ANCAs may be involved in the pathogenesis of glomerulonephritis and that the coincidence of systemic lupus erythematosus and ANCA may be responsible for the severe clinical course in our patient.