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Denaturational changes in alpha-lactalbumin result in different degrees of disordering of the protein molecule. The thermally denatured states have been studied to elucidate the energetics of residual structure and its contributions to the stability of the native conformation. The value of the heat capacity increment of alpha-lactalbumin denaturation correlates closely with the amount of residual secondary structure in the denatured protein, therefore reflecting the degree of its disordering and accessibility to solvent. As a result of the observed correlation, the behavior of protein denaturation functions is influenced by the degree of disordering of protein conformation in the denatured state. Analysis of the calorimetric data shows that the denaturational transition of alpha-lactalbumin is described by different thermodynamic functions when it proceeds to an ordered compact denatured state and to the disordered unfolded state. This difference is related to unfolding of the compact denatured state known as a molten globule state, which is populated differently under different denaturing conditions. The enthalpy and entropy of the transition from the native to the compact denatured state are always higher in magnitude than the enthalpy and entropy of the complete unfolding reaction due to the large negative hydration effect upon molten globule unfolding. Since the hydration effect increases with decreasing temperature, the gap between the partial denaturing and complete unfolding thermodynamic parameters also increases, resulting in a large difference at physiological temperatures. The results clearly indicate that a degree of residual structure in the denatured state must be taken into account to yield a more accurate description of protein structural energetics.