Exogenous nutrients do not diffuse throughout the body like a drop of dye in a beaker of water. Rather, they are allocated among tissues according to physiological rules determined by evolutionary history, physiological status, and environmental conditions. These rules also determine how endogenous nutrients are differentially mobilized and oxidized during the periods between meals. Metabolic tracers are emerging as powerful tools to address classic questions about the nutritional bioenergetics of animals. For example, which nutrients will be oxidized and which will be stored in the body? How are stored nutrients divided among the different organs and tissues? Which nutrients are mobilized between meals? When does an animal switch from one type of metabolic fuel to another? The answers to these questions surely differ among species, but also depend on complex interactions between the animal and its environment. Here I review the conceptual framework for using isotopically labeled tracers.