Network-based analysis of brain functional connections has provided a novel instrument to study the human brain in healthy and diseased individuals. Graph theory provides a powerful tool to describe quantitatively the topological organization of brain connectivity. Using such a framework, the brain can be depicted as a set of nodes connected by edges. Distinct modifications of brain network topology have been identified during development and normal aging, whereas disrupted functional connectivity has been associated to several neurological and psychiatric conditions, including multiple sclerosis, dementia, amyotrophic lateral sclerosis, and schizophrenia. Such an assessment has contributed to explain part of the clinical manifestations usually observed in these patients, including disability and cognitive impairment. Future network-based research might reveal different stages of the different diseases, subtypes for cognitive impairments, and connectivity profiles associated with different clinical outcomes.