Alzheimer's disease (AD) prominently affects the structure and function of cerebral networks. Reflecting the complex network structure of the brain, spontaneous brain activity is organized by synchronized activity across distinct temporal and spatial scales. Temporal correlations of the functional MRI (fMRI) signal during rest have been used to characterize the impact of AD on the functional connectivity of spontaneous brain activity. Here we review studies using resting-state fMRI (rs-fMRI) to explore AD-induced changes of synchronized intrinsic activity at three levels of brain organization: the regional, inter-regional and large-scale level. Changes in posterior areas of the default network (DN) and the medial temporal lobes seem to be central to AD. These areas show remarkable disturbances in neuronal communication at all spatial levels and in very early stages of the disease. Finally, rs-fMRI seems to have the potential to produce connectivity-related biomarkers that distinguish AD and healthy aging.