MHC class II molecules can exist in two conformations whIch can be distinguished on the basis of their stability in SDS. The formation of SDS-stable dimers has been shown to correlate with persistent expression of antigenic MHC class II-peptide complexes by murine antigen-presenting cells. HLA DR molecules contain either a Val or a Gly at position 86 of the β chain, which is located in a conserved and prominent hydrophobic pocket in the peptide binding site. Here we show that Va186-containing DR molecules more frequently select peptides which induce the formation of SDS stable dimers than Gly86 variants. Using analogues of the influenza virus haemagglutinin epitope 307–319 we found that the replacement of the aromatic hydrophobic anchor residue (Tyr) at position 309 by amino acids with an aliphatic hydrophobic side chain resulted in the specific formation of high numbers of SDS-stable Va186-DR but not Gly86-DR dimers. These results indicate that the fit between the first anchor residue and the hydrophobic pocket around DR β86 plays a critical role in the formation of SDS-stable DR dimers. Synthetic analogues of naturally processed DR-associated peptides displayed promiscuity in their capacity to bind to several DR specificitles and in their ability to induce the SDS-stable conformation. However, no correlation was observed between binding capacity and the ability to induce the SDS-stable conformation. Since it has been shown that SDS stability can relate to the kinetics of peptide-MHC class II interactions, the definition of the requirements for the formation of SDS-stabie HLA class II molecules may be important for the design of effective peptide-based immunomodulation protocols.