MAJOR histocompatibility complex class II molecules and their peptide ligands show unusual interaction kinetics, with slow association and dissociation rates that yield an apparent equilibrium constant of similar to 10(-6)-10(-8) M (refs 1-5). However, there is evidence for a specific, rapidly formed, short-lived complex(6). The altered migration on SDS-polyacrylamide gel electrophoresis of class II molecules upon stable peptide binding(7-9) has led to the hypothesis that the two kinetically distinguishable types of class II-peptide complexes correspond to different structures. In accord with this model, we demonstrate here that insert cell-derived HLA-DR1 class II molecules show fast, almost stoichiometric occupancy with rapidly dissociating peptide while remaining sensitive to SDS-induced chain dissociation. The same DR1 molecules slowly and quantitatively form long-lived complexes resistant to SDS-induced denaturation. Surprisingly, low-affinity interaction with peptide protects class II from denaturation at physiological temperature, a finding that has implications for understanding the role of invariant chain in the intracellular behaviour of class II molecules.