SS-B/La is a major antigenic target for autoantibodies in patients with Sjögren's syndrome. Its transient association with nascent RNA polymerase III transcripts in the cell nucleus suggest a functional role of SS-B/La in RNA processing and maturation. Human SS-B/La autoantibodies recognize at least two distinct epitopes on two separate structural domains of the SS-B/La protein and these epitopes are conserved among mammalian species. In contrast, murine monoclonal antibodies produced though immunization with purified bovine SS-B/La recognize different epitopes. To elucidate these differences, cDNA sequences of SS-B/La were cloned from several mammalian species including human, bovine, and rabbit. Complete human SS-B/La cDNAs including the coding sequence (1227bp) and untranslated sequences were isolated. The complete bovine sequence was determined from two overlapping partial cDNA clones. Comparison of the complete protein sequences encoded by the human and bovine cDNAs revealed a high degree of conservation of amino acid sequence showing only 26 substitutions/deletions out of 408 residues. RNA blot analysis indicated the presence of two size species of transcripts in bovine and rabbit cells, 1.8 kb and greater than 2.5 kb, in contrast to a single 1.8 kb mRNA species in human cells. The results of cDNA cloning support our previous finding of SS-B/La as a two-domain protein, and the RNA-binding site is confirmed to be located within N-terminal domain designated X. Epitope mapping using recombinant SS-B/La fusion proteins confirmed the findings of at least two autoepitopes located on different domains.