Functional Magnetic Resonance Imaging (fMRI) is the tool of election in the investigation of brain function in both physiological and pathological conditions. In addition to the investigation of task-evoked activity in several conditions, fMRI technique is largely used in the mapping of intrinsic Resting State (RS) BOLD fluctuations occurring in absence of task. The functional connectivity can be defined as the temporal correlation among two or more anatomically spatially remote regions and it has recently catalyzed attention in the exploration of human brain function. This technique could be implemented by several methods based on the calculation of the correlation between signal time course of one brain region and the time course of the rest, or part, of the brain. The basic assumption is that the temporal similarity between the signals in each region strongly suggests that they are in constant communication with one another constituting a functional network. Consistency of RS networks in healthy human adults is well established and changes of networks in pathological conditions is profusely studied. It has been demonstrated the existence of networks whose connection may be altered by aging or disease. The popularity of this technique belongs to different reasons. Among neuroimaging techniques, fMRI is the ideal in the investigation of functional connectivity since it has a spatial resolution superior to other methods, which is necessary to discriminate different networks. Moreover, the relative ease of data acquisition (patient are not required to perform a task) makes it a suitable approach also in a clinical environment, where, often, the most disabling diseases affect the execution of easier tasks. All these reasons, and many others of more technical aspect, made functional connectivity one of the most popular area of research in neuroscience.