Aim. To estimate the informative value of transcranial magnetic stimulation (TMS) as a tool for the functional diagnostics of motor disturbances and to evaluate its remedial potential in the patients presenting with ischemic stroke (IS) and motility disorders in the acute phase of the disease and during the early rehabilitation period. Materials and methods. The present study included the comprehensive examination of 112 patients (mean age 59.2±5.67 years) with the newly emerged hemispheric IS in the basin of the right (n=53) and left (n=59) middle cerebral artery (MCA) in the acute phase of the disease and during the early rehabilitation period associated with a moderate neurologic deficit. Moreover, TMS was used to examined 30 subjects (mean age 57.8±4.33 years) presenting without neurological pathology who comprised the control group for the comparison of the motor evoked potentials (MEP). Correlation between different MEP values and numerical score estimates of neurological deficit based on the NIH stroke scale was calculated using nonparametric Spearman's correlation coefficient. Results. In 42 (34.4%) patients with IS, MEP on the affected side were missing which was later manifested as the low rehabilitative potential for the restoration of the motor functions. In 70 of the 112 patients (65.6%) MEP were registered from the paretic limbs by TMS of the motor centers of the affected hemisphere even though with a decreased amplitude and increased latency that facilitated the well apparent recovery of the motor function during the rehabilitation process in these patients (from 5.4±0.3 points to 1.3±0.5 points, p<0.05). The persistence of MEP during TMS of the affected hemisphere in the patients with IS can be considered as the conservation of the rehabilitation potential for the recovery of the motor functions. All the time-amplitude parameters of MEP in the upper extremities significantly correlated with the NIHSS scores. In the lower extremities correlation was statistically significant for the MEP amplitude parameters and the latency difference between the affected and unaffected sides. Conclusion. TMS with the determination of the time and amplitude parameters of MEP is a sensitive method for the quantitative assessment of the functional status of the motor system in the patients presenting with ischemic stroke and motility disorders in the acute phase of the disease and during the early rehabilitation period.