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Background and purpose: Various clinical and neuroimaging predictive factors have been identified for the recovery of upper extremity (UE) motor function after stroke. However, few studies have addressed factors related to the recovery of lower extremity (LE) motor function after stroke or performed direct comparisons of UE and LE motor recovery in the same set of patients. In this study, predictive factors for UE and LE motor recovery after stroke were investigated using clinical and neuroimaging characteristics. Methods: Forty‐two subacute ischaemic stroke patients underwent structural and functional magnetic resonance imaging data acquisition and cognitive/behavioral assessments using the Fugl–Meyer assessment, the National Institutes of Health Stroke Scale (NIHSS) and the Mini‐Mental State Examination (MMSE) 2 weeks after stroke onset. Neuroimaging factors, including corticospinal tract (CST) fractional anisotropy, lesion volume, CST lesion load and interhemispheric homotopic functional connectivity, were extracted. The outcome of motor function was assessed by Fugl–Meyer assessment scores 3 months after onset. Results: Early clinical and neuroimaging factors for predicting motor recovery were noticeably different for UE and LE. UE motor function recovery was related to age, NIHSS, MMSE, CST lesion load, lesion volume, ipsilesional CST integrity and interhemispheric homotopic functional connectivity. In contrast, LE motor recovery was related to ipsilesional and contralesional CST integrity and MMSE. Specifically, LE recovery showed a strong relationship to the preservation of cognitive function compared with motor impairment. Conclusions: Our results indicate that different mechanisms underlie UE and LE motor recovery after stroke. LE motor recovery seems to be more intensively modulated by cognitive functions than UE. [ABSTRACT FROM AUTHOR]