The brain is neither uniform nor composed of similar modules but is rather a mosaic of different and highly interconnected regions. Accordingly, knowledge of functional connectivity between brain regions is crucial to understanding perception, cognition, and behavior. Functional connectivity methods estimate similarities between activity recorded in different regions of the brain. They are often applied to resting state activity, thus providing measures that are by nature task independent. The spatial patterns revealed by functional connectivity are not only shaped by the underlying anatomical structure of the brain but also partially depend on the history of task-driven coactivations. Inter-subject differences in functional connectivity may, at least to some degree, underlie variability observed in task performance across healthy subjects and in behavioral impairments in neurological patients. In this respect, recent studies have demonstrated that behavioral deficits in patients with brain injury are not only due to local tissue damage but also due to altered functional connectivity among structurally intact regions connected to the damaged site. Studies based on functional connectivity have the potential to advance basic understanding of how brain lesions induce neuropsychological syndromes. Furthermore, they may eventually suggest improved rehabilitation strategies for patients with brain injury, through the design of individualized treatment and recovery protocols.