In healthy human subjects, transcranial magnetic stimulation (TMS) applied to the motor cortex induces concurrent inhibitory and excitatory effects on motoneurone activity. In amyotrophic lateral sclerosis (ALS), a neurodegenerative disease affecting both cortical and spinal motor neurons, paired-pulse studies based on electromyographic (EMG) recording have revealed a decrease in TMS-induced inhibition. This suggested that inhibition loss may promote excito-toxicity in this disease. Against this hypothesis, an abnormally high incidence of inhibitory responses to TMS has been observed in the peristimulus time histograms (PSTHs) in ALS single motor unit studies. The disappearance of cortico-motoneuronal excitatory inputs might, however, have facilitated the detection of single motor unit inhibitory responses in the PSTHs. This question was addressed here using a new approach, where the strength of the excitatory and inhibitory effects of TMS on motoneurone activity was assessed from the duration of inter-spike intervals (ISIs). This analysis was conducted on single motor unit (MU), tested on healthy subjects and patients with ALS or Kennedy's disease (KD), a motor neuron disease which unlike ALS, spares the cortico-spinal pathway. MUs tested on KD patients behaved like those of healthy subjects unlike those tested on ALS patients. The present data reveal that in ALS, the TMS-induced inhibitory effects are truly enhanced during voluntary contractions and not reduced, as observed in paired-pulse TMS studies under resting conditions. The possible contribution of inhibitory loss to the physiopathology of ALS therefore needs to be reconsidered. The present data do not support the idea that inhibition loss may underlie excito-toxicity in ALS.