It is difficult to test responses of human motoneurons in a controlled way or to make longitudinal assessments of adaptive changes at the motoneuron level. These studies assessed the reliability of responses produced by magnetic stimulation of the corticospinal tract. Cervicomedullary motor evoked potentials (CMEPs) were recorded in the first dorsal interosseus (FDI) on two separate days. On each day, four sets of stimuli were delivered at the maximal output of the stimulator, with the final two sets at least 10 min after the initial sets. Sets of stimuli were also delivered at different stimulus intensities to obtain stimulus-response curves. In addition, on the second day, responses at different stimulus intensities were evoked during weak voluntary contractions. Responses were normalized to the maximal muscle compound action potential (Mmax). CMEPs evoked in the relaxed FDI were small, even when stimulus intensity was maximal (3.6 ± 2.5% Mmax) but much larger during a weak contraction (e.g. 26.2 ± 10.2% Mmax). CMEPs evoked in the relaxed muscle at the maximal output of the stimulator were highly reproducible both within (intraclass correlation coefficient, ICC = 0.83, session 1; ICC = 0.87, session 2) and between sessions (ICC = 0.87). ICCs for parameters of the input-output curves, which included measures of motor threshold, slope and maximal response size, ranged between 0.87 and 0.62. These results suggest that responses to magnetic stimulation of the corticospinal tract can be assessed in relaxation and contraction and can be reliably obtained for longitudinal studies of motoneuronal excitability.