Genomic investigations in animals have begun to reveal the metabolic and physiological functions of genes and protein products. However, a thorough understanding of the genomic roadmaps will require investigative approaches that yield qualitative and quantitative information on the activities, fluxes, and connectivity of pathways involved in nutrient use in farm animals; that is, the metabolic phenotype. Recently, the commercial availability of stable isotope (13C, 15N, 2H)-labeled compounds and highly accurate mass spectrometers has made it possible to probe the details of metabolic pathways involved in macronutrient use. For years, the biological sciences have exploited uniformly 13C-labeled substrates (e.g., glucose, amino acids, nucleic acids) and 13C-mass isotopomer distribution (MID) in their metabolic investigations, whereas their use in the animal sciences is very limited. When [U-13C] substrates are fed, infused, or added to cell incubations, the 13C-skeletons distribute throughout metabolic networks. 13C-Mass isotopomer distribution in intermediates and end products of the pathways provides a signature of the fluxes and activities of pathway enzymes traveled by the precursor molecule. This paper highlights aspects of animal nutrition and metabolism in which [U-13C] substrates and MID can be applied to investigations of amino acid, carbohydrate, and fat metabolism. We will focus on [U-13C] glucose as a tracer in chickens, fish, sheep, and cell cultures to investigate the interconnectivity of the pathways of macronutrient and nucleic acid metabolism, and provide demonstration of the central position of the Krebs cycle in preserving metabolic flexibility via anaplerotic and cataplerotic sequences. Exploitation of this approach in animal sciences offers endless opportunities to provide missing details of the biochemical networks of nutrient use that may prove to be strictly under genomic control.