X-ray crystallography reveals electron density in the antigen-binding site of HLA-B27 that is an interpretable image of nonameric peptides in a largely extended conformation. Clear density exists for the main chain and several side chains and is consistent with the sequence of 11 nonameric self-peptides eluted from HLA-B27. Pockets in the antigen-binding cleft bind four side chains and the amino and carboxyl termini of the peptide.