A 20-year-old Japanese woman was admitted to a hospital because of gross hematuria. She was diagnosed with IgA nephropathy with a poor prognosis, based on the formation of many crescents in the glomerulus and monocyte infiltration in the interstitium in a renal biopsy specimen in February 2003. Myeloperoxidase (MPO)-antineutrophil cytoplasmic antibody (ANCA) was not identified at that time. After treatment with high-dose steroid pulse therapy and heparin/warfarin, her urinary protein improved, to 0.5 g/day. However, 1 year after the steroid pulse therapy, urinary protein was increased to 1.2 g/day, associated with repeated episodes of tonsillitis. A second renal biopsy was performed, and showed an improving tendency, compared to the findings of the previous one, although some crescent formation and adhesions of Bowman's capsule remained. Interestingly, MPO-ANCA was positive in the serological examination done at this time. One month and a half after the second renal biopsy, she had a tonsillectomy, followed by a regimen of 5 mg oral prednisolone daily, in order to prevent the progression of IgA nephropathy. After the tonsillectomy, her urinary protein level was markedly improved, at 0.14 g/day. Her creatinine clearance was ameliorated, at 102 ml/min, and in addition, MPO-ANCA had disappeared. This case suggests that an inflammation such as tonsillitis may be associated not only with the activity of IgA nephropathy but also with the production of MPO-ANCA.