The present study examined the effects of gastric emptying rate and intestinal cell damage following a single session of endurance exercise under "hypoxic" or "normoxic" conditions at the same relative intensity. Eleven healthy males performed two trials on different days, consisting of a 60min run on a treadmill at 70% maximal running velocity (vMax) while inspiring hypoxic (FiO2: 14.5%; HYP) or normoxic air (FiO2: 20.9%; NOR). The average running velocity was 11.4 ± 0.7km/h in NOR and 10.8 ± 0.5km/h in HYP, respectively. Venous blood samples were collected to evaluate plasma intestinal fatty acid binding protein (I-FABP) as an indicator of exercise-induced intestinal cell damage. The gastric emptying rate was determined by the 13C-sodium acetate breath test. Running velocities at 70% vMax and arterial oxygen saturation were significantly lower under HYP than NOR (p < 0.001). Peak heart rate and rating of perceived exertion during exercise did not differ significantly between the trials. Maximum 13C excretion time (an indication of the gastric emptying rate) was significantly delayed in the HYP (NOR: 38.5 ± 5.0min, HYP: 45.5 ± 9.6min; p = 0.010). Furthermore, the score of nausea increased slightly, but increased significantly after exercise only in the HYP (p = 0.04). However, exercise-induced changes in plasma I-FABP, adrenaline, and noradrenaline concentrations did not differ significantly between the two trials. These results suggest that endurance exercise under hypoxic conditions impairs digestive function in the stomach compared to exercise under normoxic conditions performed at the same relative intensity.