Motor neuron diseases are disabling poor prognostic conditions, with no successful treatment. Repetitive transcranial magnetic stimulation might offer a temporary functional improvement. Objective - We intended to evaluate the extent of the functional improvement using electrophysiological and clinical tests. Methods - Patients with motor neuron disease (amyotrophic lateral sclerosis) were included. Muscle strength and respiratory function assessment represents the clinical approach, and central motor conduction time, motor unit number estimation, blink reflex and H-reflex stands for electrophysiology. Two tests were performed using the whole battery prior and after low frequency repetitive transcranial magnetic stimulation, using 1 Hz stimulation frequency for five consecutive days, 20 minutes daily, at 80% of the individual resting motor threshold. Results - Central motor conduction time, muscle strength and pulmonary function showed no statistically significant differences, but a tendency towards improvement. Motor unit number estimation, blink reflex and H-reflex showed a significantly better outcome after the five day repetitive transcranial magnetic stimulation treatment. Conclusion - Low frequency repetitive transcranial magnetic stimulation influences beneficially electrophysiological parameters in amyotrophic lateral sclerosis, but with little clinical impact; further studies are needed to validate the extent of the effect.