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Background and Purpose: High-frequency repetitive transcranial magnetic stimulation (rTMS) aids motor recovery in patients with subacute stroke. However, the response to high-frequency rTMS is highly variable between patients. The aim of this study was to identify the factors associated with improved motor function in response to high-frequency rTMS in subacute stroke patients with moderate to severe upper extremity motor involvement. Methods: Sixty-two patients with subacute stroke were enrolled. rTMS was applied over the primary motor cortex of the affected hemisphere at 10 Hz with 1,000 pulses/day for 10 days. Upper limb motor function was scored with the upper limb of Fugl-Meyer Assessment (FMA-UL) score before intervention and immediately after intervention. All FMA-UL changes greater than or equal to 5 points were considered clinically significant. Potential influencing factors considered included patient characteristics, motor function, corticospinal tract (CST) integrity assessments, and genetics. Multivariate logistic regression analysis was used to identify the significance of each of these factors. Results:We found that the two factors with the greatest impact on the improvement in FMA-UL score were: 1) the functional integrity of the CST, and 2) the brain-derived neurotrophic factor (BDNF) genotype (p < 0.05). Age tended to influence clinically significant changes in the FMA-UL score, although this effect was not significant. Conclusion: Our findings suggest that high-frequency rTMS interventions aimed at improving upper extremity motor function in patients with subacute stroke with moderate to severe motor involvement should be individually tailored according to functional CST status and BDNF genotype. [ABSTRACT FROM AUTHOR]