Organic compounds generated by biological processes, either at the surface or within the Earth' s crust, are incorporated into many types of geologic materials and undergo numerous transformations driven by changes in temperature, pressure, and composition. These transformations reflect the energetic response of compounds that are transported by geologic processes into conditions where they are far from equilibrium. The active geochemical processes and the geologic variables that influence the course of organic alteration can be identified by evaluating the energy differences between the starting compounds and their alteration products in deeply buried sedimentary rocks, ore deposits, petroleum, and elsewhere. Thermodynamic calculations provide quantitative assessments of these energetic differences, and it is the purpose of this review to illustrate how such calculations can reveal the driving forces of organic transformations. This type of approach can be useful in the study of ore deposits because oxidation-reduction reactions dictate the course of organic alteration. These redox reactions can couple to inorganic redox processes that enhance metal transport or trigger ore deposition. As always, thermodynamics indicates the possible, and cannot, on its own, reveal the mechanisms through which the transformations may occur. Nevertheless, thermodynamics provides the means to assemble plausibility arguments based on geologic information and to test those arguments with an independent set of data.