Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used by athletes to reduce exercise-induced inflammation and pain. However, NSAID use has been linked to side effects, including mucosal damage in the gastrointestinal tract resulting in endotoxemia and inflammation. Incidentally, when NSAID use is combined with exercise there is some evidence that this effect may be exacerbated; however, this hypothesis has not been directly tested in a controlled experiment. We examined the combined effect of indomethacin (IND) and exercise on muscle and brain inflammation in mice. Male C57BL/6 mice were randomly assigned to: Exercise 0 mg/Kg IND (Ex-0), Sedentary 0 mg/Kg IND (Sed-0), Exercise 2.5 mg/Kg IND (Ex-2.5), or Sedentary 2.5 mg/Kg IND (Sed-2.5) (n=8-11/group). Mice were given IND (gavage) 1 h before exercise (treadmill run at 25 m/min, 8% grade for 90 min) or rest for 5 consecutive days. Run times and body weight were recorded daily. Muscle and brain were examined for gene expression of inflammatory mediators after 5 days of treatment. While IND and exercise alone had little effect on inflammation, the combination treatment produced substantial increases in the muscle (IL-1β, MCP-1 & TNF-α) and brain (IL-1β & MCP-1) (P<0.05). Hematocrit and hemoglobin were decreased along with body weight (days 3-5), and run time to fatigue (days 3-5) (P<0.05) and in general, these were correlated with the increased expression of muscle and brain inflammatory mediators. The combination of IND and exercise can lead to inflammation in both the muscle and brain that is associated with serious side effects and impaired performance in mice.