To evaluate potential differences in protein A among Staphylococcus aureus strains, lysostaphin-solubilized cell wall proteins from 12 serologically distinct strains were analyzed by 7.5% sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). Seven presumptive protein A variant identified in the 45- to 57-kilodalton range were then studied for qualitative binding affinities to nonimmune mouse and rabbit immunoglobulin G (IgG) by enzyme-linked immunoelectrotransfer blot. Essentially, all presumptive protein A variants demonstrated binding to both nonimmune rabbit and mouse IgG and had differential binding to mouse monoclonal IgG1 at pH 8.2 than at 5.5. Because of Fc-binding properties and molecular weight similarity to the well-characterized Cowan I protein A, these proteins appeared to represent protein A variants. Amino sugar analysis (less than 1%) by reverse-phase high-pressure liquid chromatography suggested that the apparent molecular weight differences in protein A were not due to associated mucopeptides. Further differences in protein A variants were studied by peptide mapping. Each of the seven protein A variants, distinguishable on SDS-PAGE, also produced distinct peptide cleavage patterns. In addition, two protein A variants indistinguishable on SDS-PAGE could be further subdivided by peptide mapping. These results suggest that SDS-PAGE analysis of protein A, particularly in conjunction with peptide mapping, may be useful in distinguishing distinct strains of S. aureus. Different protein A variants may also have unique functional or immunologic capabilities.