Functional and structural neuronal networks, as recorded by resting-state functional MRI and diffusion MRI-based tractography, gain increasing attention as data driven whole brain imaging methods not limited to the foci of the primary pathology or the known key affected regions but permitting to characterize the entire network response of the brain after disease or injury. Their connectome contents thus provide information on distal brain areas, directly or indirectly affected by and interacting with the primary pathological event or affected regions. From such information, a better understanding of the dynamics of disease progression is expected. Furthermore, observation of the brain's spontaneous or treatment-induced improvement will contribute to unravel the underlying mechanisms of plasticity and recovery across the whole-brain networks. In the present review, we discuss the values of functional and structural network information derived from systematic and controlled experimentation using clinically relevant animal models. We focus on rodent models of the cerebral diseases with high impact on social burdens, namely, neurodegeneration, and stroke.