The differential scanning calorimetry analysis of the murine MHC class II molecule, I-Ek, in complex with an antigenic peptide derived from mouse hemoglobin (Hb), showed that the thermal stability at the mildly acidic pH is higher than that at the neutral pH. Although the thermal unfolding of I-Ek-Hb was irreversible, we extracted the equilibrium thermodynamic parameters from the kinetically controlled heat capacity curves. Both the denaturation temperatures and the enthalpy changes were almost independent of the heating rate over 1°C per min. The linear relation between the denaturation temperature and the calorimetric enthalpy change provided the heat capacity changes, which are classified into one for mildly acidic pH region and another for the neutral pH region. The equilibrium thermodynamic parameters showed that the increased stability at the mildly acidic pH is due to the entropic effect. These thermodynamic data provided a new insight into the current structural model of a transition to an open conformation at the mildly acidic pH, which is critical for the peptide exchange function of MHC class II in the endosome.