The possibility that viruses play a role in the etiology of various autoimmune diseases has been proposed. One approach to the search for these agents involves identifying potential crossreactive epitopes in viruses that infect cells of the immune system or of the target tissues. Antibodies to DNA topoisomerase I are the marker autoantibodies for diffuse systemic sclerosis. The major epitope of the antigen was therefore sought through cloning and sequencing of the cDNA for human topoisomerase I and eventually by the synthesis of the smallest possible peptide recognized by sera from patients with the diffuse form of systemic sclerosis. The antigenic 11-amino acid sequence contains 6 sequential amino acids that are identical to a sequence present in the group-specific antigen (p30gag) of some mammalian retroviruses. This sequence is separated by only 1 amino acid from the retroviral epitope sequence that crossreacts with autoantibodies against the marker antigen for mixed connective-tissue disease and systemic lupus erythematosus, the 70-kDa polypeptide of U1 ribonucleoprotein particles. These findings suggest that a retroviral agent may be involved in the pathogenesis of systemic sclerosis and other connective tissue diseases and that antibodies to intracellular antigens are not involved in the pathogenesis of autoimmune disease but may be useful as footprints for tracking the potential etiological agent of autoimmune disease.