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The present study aimed to identify the brain regions involved in upper and lower limb motor and functional recovery after stroke.Twenty-five patients (mean age 73.4 years; average duration from stroke onset 50.1 months) were examined. Fractional anisotropy (FA) mapping using diffusion tensor imaging, and clinical measures, including the Fugl–Meyer motor assessment of upper and lower limbs, the Modified Barthel Index (MBI), and Functional Ambulation Category, were used for examinations. Linear regression analyses were carried out with the FA map as a dependent variable, each clinical measure as an independent variable, and patient age as a covariate.FA in the internal capsule of the posterior limb of the lesioned hemisphere was significantly associated with Fugl–Meyer motor assessment scores for the upper limbs, whereas FAs in the internal capsule of the posterior limb of the lesioned hemisphere, the posterior corpus callosum of the lesioned hemisphere, and the middle cerebellar peduncle of the contralateral hemisphere were associated with Fugl–Meyer motor assessment scores for the lower limb. FA in brain regions with bilateral connection fibers was commonly associated with the score on the Korean version of the MBI and participants’ functional ambulation. Furthermore, the FA in the corticospinal tract in the contralesional hemisphere was also associated with the score on the Korean version of the MBI (corrected P<0.05).Motor and functional recovery of upper and lower limbs involves different brain regions. This finding is of particular relevance for treatment and recovery in stroke.