The aim. This study describes the difference of transcranial magnetic stimulation (TMS) indicators among patients with different courses of multiple sclerosis (MS) and Expanded Disability Status Scale (EDSS), usage of motor evoke potentials (MEP) and motor threshold (MT) indicated by paired TMS stimulation. Materials and methods. 130 patients with MS were examined neurologically by usage of EDSS. TMS was performed on 96 patients with MS. TMS inventory included magnetic coil 90 mm that was connected to TMS stimulator machine. Pulses from the abductor major muscle of the dominant upper limb were recorded by electromyography device. TMS parameters included MT, cortical MEP and MEPs recorded on 2, 3, 12 and 15 seconds after delivered stimulus. Results. Comparison between groups of different EDSS showed significant difference of MT: higher EDSS had higher MT. When data was divided into MS types, significant negative correlation was found in group of PMS between EDSS and MEP amplitude 1 (r=–0.43; p=0.018), MEP2 (r=–0.45; p=0.072), MEP3 (r=–0.41; p=0.05), MEP4 (r=–0.51; p=0.018). Conclusion. The relationship between EDSS, disease course and TMS electrophysiological parameters might be useful in usage of paired TMS as a tool to show the cortical degeneration. It is a perspective direction in future research of finding additional tool for MS prediction.