Stable isotopes are becoming an increasingly powerful tool for studying the physiological ecology of animals. The (13)C/(12)C 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 (13)C/(12)C ratio of exhaled CO(2) to determine substrate digestion and oxidation, we found little evidence that animal physiologists or physiological ecologists have applied (13)C/(12)C breath analysis in their studies. The analysis breath (13)C/(12)C 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 breath(13)C/(12)C 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 (13)C/(12)C ratios in exhaled CO(2) 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.