Chemical information available in organisms can be categorized into three major domains, macromolecular, small molecules, and isotope ratios. Information about physiological state is commonly obtained by qualitative and quantitative analysis in the macromolecular and small molecule domains. Genomics and proteomics are emerging approaches to analysis of macromolecules, and both areas yield definitive information on present physiological state. There is relatively little record of past physiological states of the individual available in these domains. Natural isotopic variability, particularly on an intramolecular level, is likely to retain more physiological history. Because of ubiquitous isotopic fractionation, every stereochemically unique position in every molecule has an isotope ratio that reflects the processes of synthesis and degradation. This fact highlights a vast amount of organismal chemical information that is essentially unstudied. Isotope measurements can be classified according to the chemical complexity of the analyte into bulk, compound-specific, and position-specific or intramolecular levels. Recent advances in analysis of isotope ratios are transforming natural science, and particularly answering questions about ecosystems using bulk methods; however, they have had relatively little impact on physiology. This may be because the vast complexities of physiological questions demand very selective information available in position-specific isotope analysis (PSIA). The relatively few high-precision PSIA studies, based on isotope ratio mass spectrometry (IRMS), have revealed intramolecular isotope ratio differences in pivotal physiological compounds including amino acids, glucose, glycerol, acetate, fatty acids, and purines. The majority of these analyses have been accomplished by laborious offline methods; however, recent advances in instrumentation presage rapid PSIA that will be necessary to attack real physiological problems. Gas-phase pyrolysis has been shown to be an effective method to determine 13C/12C at high precision for molecular fragments, and technologies to extend C-based PSIA to N and other organic elements are emerging. Two related efforts are warranted, (a) development of rapid, convenient, and sensitive methods for high-precision PSIA, a necessary precursor to (b) a concerted investigation into the relationship of metabolic state to intramolecular isotope ratio. Inherent in this latter goal is the need to identify long-lived molecules in long-lived cells that retain a record of early isotopic conditions, as has been shown for post-mortem human neuronal DNA. Using known metabolic precursor-product relationships between intramolecular positions, future studies of physiological isotope fractionation should reveal the relationship of diet and environment to observed isotope ratio. This science of isotope physiology, or simply isotopics, should add an important tool for elucidation of early factors that effect later health, probably the most difficult class of biomedical issues. Copyright © 2001 John Wiley & Sons, Ltd.