To further define motor nervous system alterations in myotonic dystrophy (MD), motor potentials to transcranial and cervical magnetic stimulation (MEPs) were recorded from the right abductor pollicis brevis muscle in 10 patients with MD and in 10 healthy controls. Cortical and cervical latencies, central motor conduction time (CMCT), stimulus threshold intensity and cortical MEP amplitudes expressed both as absolute values and as %M were analysed. MEP cervical latency, absolute or relative amplitude and excitability threshold did not significantly differ in patients and controls. The mean cortical motor latency and CMCT were significantly prolonged in MD patients with respect to normal subjects. Moreover, CMCTs were found to be significantly related to stimulus threshold intensity (P = 0.03) and only marginally related to absolute cortical amplitude (P = 0.06). These findings are indicative of a central motor delay, also related to decreased excitability of motor neurons, in patients with MD. No correlations were found between individual neurophysiological parameters and age, duration of disease and clinical impairment. Our results suggest that magnetic stimulation studies can detect subclinical dysfunctions of the central motor system in MD patients, as one of the multisystemic manifestations of the disease, rather independent of the primitive muscle damage.