Brain tryptophan (TRP) concentrations and serotonin (5HT) synthesis and release increase during running. This increase in 5HT function may promote central fatigue and contribute to suboptimal physical performance. The rise in brain TRP is reputed to result from exercise-induced elevations in serum nonesterified fatty acid (NEFA) concentrations, which dissociate TRP from albumin in blood and increase the serum free TRP pool. But, as discussed in this article, ample evidence exists that the serum free TRP pool does not control brain TRP uptake. The clearest data are dietary, but pharmacologic data in exercising rats also support this conclusion. Changes in the serum levels of amino acids that compete with TRP for brain uptake appear also not to explain the rise in brain TRP. The mechanism is therefore not presently known. The link between the rise in brain TRP and 5HT synthesis/release is not simple: a rise in brain TRP stimulates 5HT synthesis/release in actively firing neurons. Hence, during exercise, only 5HT neurons that are firing should increase 5HT production/release when brain TRP rises. It is not known which 5HT neurons fire during exercise; the 5HT neurons that respond to exercise-induced increases in brain TRP are therefore not known. Hence, it is not possible to conclude which 5HT neurons contribute to the generation of central fatigue. Because some 5HT neurons control specific functions important to physical performance (e.g., respiration), the current understanding of 5HT neuronal function in central fatigue might benefit from the study of specific 5HT pathways during exercise.