Spontaneous restoration of function after stroke is associated with remodelling of functional neuronal networks in and around the ischemic lesion. However, the spatiotemporal profile of structural alterations in (peri)lesional tissue in relation to post-stroke recovery of neuronal function remains largely to be elucidated. We performed neurological testing in combination with in vivo serial T(2)-weighted magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) to assess functional recovery in relation to longitudinal changes in tissue integrity from 3 h up to 9 weeks after experimental unilateral stroke in rats (n=7). Subsequently, to evaluate perilesional neuronal connectivity, we conducted manganese-enhanced MRI after MnCl(2) injection in cortical tissue at the boundary of the lesion at 10 weeks post-stroke (n=5). All animals showed significant improvement of neurological function over time. Normalization of tissue T(2) and fractional diffusion anisotropy (FA) after significant subacute change was observed in cortical and subcortical lesion borderzones between 3 and 9 weeks post-stroke. Progressive FA increase above baseline levels was detected in perilesional white matter areas (n=4). In these animals particularly, significant manganese enhancement appeared within the neuronal network around the chronic lesion, including areas that were part of the lesion at day 3 post-stroke. This longitudinal multi-parametric MRI study suggests that resolution of early ischemic damage and reorganization of white matter in perilesional tissue is chronically accompanied by preservation or restoration of neuronal connectivity, which may significantly contribute to post-stroke functional recovery.