Protein A is a cell wall linked protein of Staphylococcus aureus that binds mammalian IgG. Although protein A displays high size heterogeneity among strains, cloning and sequencing of its gene from two strains had not shown a large difference in size. Here we report a third protein A gene sequence that shows a size variation relative to these two, due to deletions on both one IgG binding domain and a cell wall binding domain (region X). By analysis of the three sequences we were able to delineate a hypothetic model for region X domain evolution and discussed the origin of genetic variability within and without strains.