Stroke is the leading global cause of disability and the third most common cause of death. Between 55% and 75% of subjects who suffered a stroke have functional motor limitations present even 3-6 months after the event, which affects their quality of daily life. Transcranial magnetic stimulation (TMS) allows modelling of adaptive brain mechanisms, and genetic variations could explain the degree of post-stroke recovery. Hence the idea of a study of TMS-based neuroplasticity and investigation of rs6265 polymorphism of the BDNF gene in subjects with acute ischemic stroke. A controlled clinical study was performed in 95 subjects after stroke in the vascular territory of the middle cerebral artery, aged between 37 and 94 years, using the repetitive 1Hz SMT protocol, applying 7 clinical evaluation scales (NIHSS, Orpington, MRC, MRS, Mini-Mental Test Score, Barthel and 9-Peg Hole Test) and performing Sanger sequencing of the BDNF gene. It was observed that the dynamics of the TMS group is clearly superior according to all scales applied, regardless of topographic level, timing, age and sex (p <0.05), and the lack of rs6265 polymorphism is a positive indicator for recovery from ischemic stroke in the acute phase, highlighting the role of the human BDNF gene as a potential genetic biomarker of neuroplasticity. Our study identified some traits of the ideal candidate for TMS in after-stroke rehabilitation, as: the presence of motor evoked potential immediately after the stroke onset and the absence of rs6265 polymorphism in the BDNF gene – that could be set as individual markers in order to modulate personalized neurorecovery interventions.