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.