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We review and discuss methods for including the role of point defects in calculations of the free energy, composition and phase stability of elements and compounds. Our principle aim is to explain and to reconcile, with examples, the perspectives on this problem that are often strikingly different between exponents of CALPHAD, and others working in the overlapping fields of physics, chemistry and materials science. Current methodologies described here include the compound energy formalism of CALPHAD, besides the rather different but related canonical and grand-canonical formalisms. We show how the calculation of appropriate defect formation energies should be formulated, how they are included in the different formalisms and in turn how these yield equilibrium defect concentrations and their contribution to free energies and chemical potentials. Furthermore, we briefly review the current state-of-the-art and challenges in determining point defect properties from first-principles calculations as well as from experimental measurements.