The kinetics of the reactions of peptides with class II proteins of the major histocompatibility complex (MHC) are simulated so as to include the spontaneous inactivation of peptide-free MHC proteins. These simulations include the kinetics of loss of endogenous peptides normally present in preparations of these proteins and, in some cases, the formation of kinetic intermediates in the binding of added peptides to peptide-free proteins. In these reactions the amount of complex between the MHC protein and added peptide does not represent an equilibrium state of the system but rather a quasistationary concentration that is the result of a competition between peptide binding and inactivation of the peptide-free protein. It is shown that in spite of these complex kinetics. Scatchard plots of simulated binding data are frequently linear, as observed experimentally. However, the "equilibrium constants" derived from the slopes of such plots bear no simple relationship to the true equilibrium constants for the reactions.