MRI is a vital tool for the measurement of acute stroke and has been used to visualize changes in activation patterns during stroke recovery. There is emerging interest on using MRI to monitor the structural substrates of spontaneous recovery and neurorestorative treatment of stroke. In this review, we describe the use of MRI and its associated challenges to measure vascular and neuronal remodeling in response to spontaneous and therapy-induced stroke recovery. We demonstrate that MRI methodologies may be used in real-time monitoring of recovery from stroke.