IEF, using 6 M urea, provides a unique opportunity to analyze the spectrotypes of antibodies in immune complexes (IC) in vivo. Using this technique, we have analyzed the clonotypes of anti-DNA antibodies expressing specific Id in the circulating IC of patients with active lupus nephritis. Serum anti-ssDNA and anti-dsDNA antibodies showed heterogeneous spectrotypes. The antibodies isolated from circulating IC had a restricted clonotype and a neutral charge and were directed mainly to ssDNA and, to a lesser extent, to dsDNA. These samples failed to form complexes with DNA when they were subjected to absorption to a DNA-coupled Sepharose column. Anti-DNA antibodies expressed specific Id, termed O-81 or NE-1, which were detected only in the IC of patients with active lupus nephritis. Anti-DNA clonotypes, including O-81 and NE-1 idiotypes, were also found in the eluates of renal glomeruli of lupus patients. These results indicate that subpopulations of anti-DNA antibodies in circulating IC are limited, and may play an important role in the pathogenesis of lupus nephritis.