Naturally occurring autoantibodies are ubiquitous and may serve physiological functions. We examined the relationship of natural and disease-associated autoantibodies in the context of autoantibodies to dihydrolipoamide acetyltransferase, the 74 kDa E2 sub-unit of the mitochondrial pyruvate dehydrogenase complex (PDC-E2), characteristic of primary biliary cirrhosis (PBC). We tested for natural autoantibodies to PDC-E2 in normal sera, and compared epitopes recognised by natural and disease-associated autoantibodies. Methods included affinity purification of anti-PDC-E2 from normal and PBC sera, ELISA and immunoblotting, capacity of antibodies to inhibit the enzyme function of the pyruvate dehydrogenase complex (PDC), use of F(ab)(2) fragments of anti-PDC-E2 in inhibition assays, and testing affinity purified anti-PDC-E2 on peptide fragments of PDC-E2. We found that natural autoantibodies to PDC-E2 of IgG class were demonstrable in all healthy human sera (10/10). However, their reactivity differed from that of disease-associated autoantibodies, in that anti-PDC-E2 from normal serum failed to inhibit the catalytic activity of PDC; and F(ab)(2) fragments from PBC sera potently blocked the binding of anti-PDC-E2 from PBC sera to PDC-E2, but not the binding of natural anti-PDC-E2 to PDC-E2. Immunoblotting on fragments of PDC-E2 using affinity-purified preparations from PBC sera and normal sera failed to provide evidence for gross differences in epitope reactivity. We conclude that normal human sera contain natural IgG autoantibodies to the immunodominant inner lipoyl domain of PDC-E2, as seen characteristically in PBC. However, there is evidence for differences in fine epitope recognition. (C) 1998 Academic Press Limited.