Whereas morphological MR imaging provides clear evidence of white and gray matter lesions reflecting multiple sclerosis (MS) pathology, functional MRI (fMRI) studies of the motor, visual and cognitive networks in MS patients have provided evidence of more diffuse cortical changes. Compared with healthy subjects, fMRI changes are characterized by expansion within physiological task-related networks, such as more prominent participation of higher-level areas or recruitment of additional areas, as well as differences in resting state networks and disrupted within-network connectivity. Longitudinal fMRI studies have demonstrated that the observed abnormalities vary over the course of the disease, even in patients in disease remission (i.e., outside of relapses). Treatment interventions, such as treatment of leg spasticity with intramuscular botulinum toxin, may cause notable, even if transient, normalization of task-related networks. Functional MRI changes in MS reflect morphological MRI abnormalities, especially when more sensitive techniques are applied to detect normal-appearing white and gray matter of the brain and spinal cord. This phenomenon fits in the more widely described mechanism of increased recruitment within functional networks to at least partially compensate for structural damage in brain diseases as diverse as stroke and amyotrophic lateral sclerosis ( Weiller et al., 2006 ). While notable progress has been made to improve prognosis of the clinical course of MS using sophisticated morphological markers, e.g., ( Kalincik et al., 2012 , Zivadinov et al., 2013 ), functional MRI might also contribute to improve disease monitoring prognosis. Finally, functional MRI may be used to study the effects of different therapies on central nervous system engagement ( Filippi and Rocca, 2013 ).