The major histocompatibility complex (MHC) class II molecules are highly polymorphic membrane glycoproteins that bind peptide fragments of proteins and display them for recognition byCD4+ T ceils. To understand the effect of human MHC class II polymorphism on peptide-MHC interaction, we have isolated Ml3 phage from a large Ml3 peptide display library by selection with DRBl l 0401 and DRBI* 1101 molecules, as recently described for DRBI* 0101. Sequence analysis of the peptlde-encoding region of DR-bound phage led to the identification of position-specific anchor residues, defining motifs for peptide binding to DR molecules. The three DR motifs share two anchor residues at relative positions 1 and 4, while allele-specific anchor residues have been identified at position 6. These results provide a biophysical basis for both the promiscuity and the specificity of peptide recognition by DR molecules.