Autoimmunity to DNA in mouse models for the systemic autoimmune disease systemic lupus erythematosus (SLE) has all of the characteristics of an Ag-driven secondary immune response to DNA. Since the pathogenesis of anti-DNA Ab in SLE is correlated to Ab specificity for native DNA (dsDNA), understanding how such specificity is generated is important. As with immune A responses to most Ags, autoimmune Ab responses to DNA are dependent upon the clonal selection of B cells expressing particular H and L chain V-region structures. The VH structures of most autoimmune anti-DNA Abs include at least one arginine in VH-CDR3; moreover, previous results led us to propose that anti-DNA Ab specificity for dsDNA may be dependent upon the relative position of arginines in VH-CDR3. The present results demonstrate a strong correlation between specificity for dsDNA and arginine position in VH-CDR3, for Abs with V, encoded by VH genes from the VH7183, VHQ52, and VHS107 families but not from the VH558 family. Specificity for dsDNA was not only correlated to the presence of VH-CDR3 arginines but also to the relative position of the arginines in VH-CDR3. The majority of the VH-CDR3 arginines appeared to have been encoded by sequences generated during V-D-J recombination. These results are not only important for understanding how A specificity for dsDNA is generated but also how somatically derived structures generated during V-D-J recombination may influence clonotype selection of an immune response within an individual mouse.