The human MHC class II molecule encoded by DQA1*0102/DQB1*0602 (termed DQ0602) confers strong susceptibility to narcolepsy (161400) but dominant protection against type I diabetes. To elucidate the molecular features underlying these contrasting genetic properties, Siebold et al. (2004) determined the crystal structure of the DQ0602 molecule at 1.8-angstrom resolution. Structural comparisons to homologous DQ molecules with differential disease associations highlighted a previously unrecognized interplay between the volume of the P6 pocket and the specificity of the P9 pocket, which implies that presentation of the expanded peptide repertoire is critical for dominant protection against type I diabetes. In narcolepsy, the volume of the P4 pocket appears central to the susceptibility, suggesting that the presentation of a specific peptide population plays a major role.