Because the natural enrichment of carbohydrate with 13C is greater than that of lipid, we hypothesized that the natural enrichment of exhaled CO2 with 13C (EN) could be used to gauge endogenous substrate utilization in exercising human subjects. To test this, EN and the respiratory exchange ratio (R) which equals the respiratory quotient (RQ) in the steady state, were measured simultaneously in seven subjects. Rest and exercise protocols, performed under conditions of room air (sea level) and hypoxic (inspired O2 fraction = 0.15) breathing, were chosen to cause a variety of patterns of oxidative substrate utilization. Work rates were performed both below and above the subject's lactate threshold (LT). Work above the LT was expected to cause the greatest increase in EN reflecting greater utilization of glucose. There was significant intersubject (P less than 0.05) but not intrasubject variability in resting EN. By 40 min of exercise, EN increased significantly (P less than 0.05) over resting values in all exercise protocols during both room air and hypoxia conditions. In the room air studies, we found no difference in EN during the below-LT work, even though there were significant increases in O2 uptake (VO2). In contrast, above-LT work resulted in significantly greater increases in EN by 20 and 40 min of exercise (P less than 0.05). Contrary to our expectations, we observed no separate effect by hypoxia on the EN during exercise. Both EN and R tended to increase from rest to exercise, but during exercise there was no overall correlation between R and the EN. EN reflects changes in endogenous substrate utilization over relatively long periods of time such as at rest, but delays in the appearance of 13CO2 at the mouth due to dilution in body CO2 pools, and possibly isotopic fractionation, preclude the usefulness of EN as an indicator of endogenous fuel mix during short-term exercise.