The stable isotope compositions of biologically precipitated apatite in bone, teeth, and scales are widely used to obtain information on the diet, behavior, and physiology of extinct organisms and to reconstruct past climate. Here we report the application of a new type of geochemical measurement to bioapatite, a "clumpedisotope" paleothermometer, based on the thermodynamically driven preference for 13 C and 18 O to bond with each other within carbonate ions in the bioapatite crystal lattice. This effect is dependent on temperature but, unlike conventional stable isotope paleothermometers, is independent from the isotopic composition of water from which the mineral formed. We show that the abundance of 13 C-18 O bonds in the carbonate component of tooth bioapatite from modern specimens decreases with increasing body temperature of the animal, following a relationship between isotope "clumping" and temperature that is statistically indistinguishable from inorganic calcite. This result is in agreement with a theoretical model of isotopic ordering in carbonate ion groups in apatite and calcite. This thermometer constrains body temperatures of bioapatite-producing organisms with an accuracy of 1-2°C. Analyses of fossilized tooth enamel of both Pleistocene and Miocene age yielded temperatures within error of those derived from similar modern taxa. Clumped-isotope analysis of bioapatite represents a new approach in the study of the thermophysiology of extinct species, allowing the first direct measurement of their body temperatures. It will also open new avenues in the study of paleoclimate, as the measurement of clumped isotopes in phosphorites and fossils has the potential to reconstruct environmental temperatures.apatite | isotope | paleoclimate | thermophysiology | paleothermometry T he mechanisms by which animals regulate their body temperatures are among the most fundamental aspects of their biology. The acquisition of endothermy, the ability to maintain high and stable body temperatures through internal heat production, is a major physiological change that occurred at an unknown stage during the evolutionary transition to mammals and birds from their ancestors among the nonmammalian therapsids and nonavian dinosaurs, respectively (1). Approaches to understanding the physiology of extinct animals and the evolution of endothermy have largely focused on biophysical modeling, anatomical observations, growth rate analysis from bone histology, and behavioral studies such as estimating predator/prey ratios (1-7). The validity of each of these approaches is uncertain (for contrasting viewpoints on approaches to dinosaur thermoregulation see refs. 4 and 5).Modern endothermic mammals and ectotherms, such as alligators and crocodiles, generally have significant differences in average body temperatures. With rare exceptions, mammals have high and stable body temperatures around 36-38°C regardless of their environment, whereas the body temperatures of ectotherms are generally lower on average and often fluctuate depending o...