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A comparative site-directed mutagenesis study of staphylococcal enterotoxins A and B was undertaken to identify key amino-acid residues which govern interactions with major histocompatibility class II molecules. This involved generating a three-dimensional homology model for enterotoxin A in complex with the HLA-DR1 molecule, based on the reported X-ray crystal structures of enterotoxin B, both free and bound to HLA-DR1. A binding motif previously described for enterotoxin B was found to be conserved in enterotoxin A. An examination of the experimental data with the homology model clarifies how T-cell responses to enterotoxin A, and most bacterial superantigens, are likely to be mediated by variations of a structurally conserved HLA-DRα binding motif.