Stable isotopes are becoming an increasingly powerful tool for studying the physiological ecology of animals. The 13C/12C ratios of animal tissues are frequently used to reconstruct the diet of animals. This usually requires killing the subjects. While there is an extensive medical literature on measuring the 13C/12C ratio of exhaled CO2 to determine substrate digestion and oxidation, we found little evidence that animal physiologists or physiological ecologists have applied 13C/12C breath analysis in their studies. The analysis breath 13C/12C ratios has the advantage of being non-invasive and non-destructive and can be repeatedly used on the same individual. Herein we briefly discuss the medical literature. We then discuss research which shows that, not only can the breath13C/12C ratio indicate what an animal is currently eating, but also the animal's diet in the past, and any changes in diet have occurred over time. We show that naturally occurring 13C/12C ratios in exhaled CO2 provides quantitative measure of the relative contribution of carbohydrates and lipids to flight metabolism. This technique is ripe for application to field research, and we encourage physiological ecologists to add this technique to their toolbox.