The theory of the binding polynomial constitutes a very powerful formalism by which many experimental biological systems involving ligand binding can be analyzed under a unified framework. The analysis of isothermal titration calorimetry (ITC) data for systems possessing more than one binding site has been cumbersome because it required the user to develop a binding model to fit the data. Furthermore, in many instances, different binding models give rise to identical binding isotherms, making it impossible to discriminate binding mechanisms using binding data alone. One of the main advantages of the binding polynomials is that experimental data can be analyzed by employing a general model-free methodology that provides essential information about the system behavior (e.g., whether there exists binding cooperativity, whether the cooperativity is positive or negative, and the magnitude of the cooperative energy). Data analysis utilizing binding polynomials yields a set of binding association constants and enthalpy values that conserve their validity after the correct model has been determined. In fact, once the correct model is validated, the binding polynomial parameters can be immediately translated into the model specific constants. In this chapter, we describe the general binding polynomial formalism and provide specific theoretical and experimental examples of its application to isothermal titration calorimetry.