It is unknown whether changes in corticomotor excitability follow prolonged exercise in healthy humans. Furthermore, the role of supraspinal fatigue in decrements of force production and voluntary activation following prolonged exercise has not been established. This study investigated peripheral and central fatigue after a marathon (42.2 km) on a treadmill. Isometric ankle dorsiflexion force and electromyographic responses of the tibialis anterior in response to magnetic stimulation of the peroneal nerve (PNMS) and the motor cortex (TMS) were measured before, immediately after, 4 and 24 h post-marathon (MAR) in nine volunteers (mean +/- s.d. completion time, 208 +/- 22 min). Maximal voluntary contraction decreased by 18 +/- 7% immediately after MAR (P = 0.009) and remained significantly decreased after 4 h. The amplitude of the evoked response to TMS, but not to PNMS, was depressed immediately post-MAR by 57 +/- 25% (P = 0.04). Potentiated resting twitch force was reduced in response to both TMS and PNMS post-MAR (71 +/- 8 and 35 +/- 2% decrease, P = 0.035 and 0.037, respectively), and voluntary activation was reduced to 61.9 +/- 18% immediately post-MAR (P < 0.05). All measures had returned to baseline values after 24 h. These results suggest that fatigue was attributable to both a disturbance of the contractile apparatus within the muscle and submaximal output from the motor cortex.