Abstract Anti-DNA autoantibodies are the hallmark of the autoimmune disease systemic lupus erythematosus. Although these antibodies are both diagnostic and pathogenic, little is known about their structures and the manner in which they recognize DNA antigens. To address the first of these points we have predicted the three-dimensional structures of 40 monoclonal anti-DNA F(ab) fragments derived from lupus-prone mice. These antibodies were chosen to encompass several different autoimmune strains along with the known variable region gene families that encode anti-DNA. We find that the structures of the antigen binding regions of these antibodies fall into three main classes, irrespective of both the mouse strain and genetic origins of the antibody. Specifically, high-affinity anti-ssDNA appear to possess a narrow channel that is presumably used for ligand recognition, whereas the binding site on anti-dsDNA is an open surface that is large enough to accommodate a DNA duplex. These findings provide structural data to support the hypothesis that anti-DNA arise by DNA-driven B cell activation and clonal expansion.