The diagnosis and management of patients with persistent vegetative (PVS) and minimally conscious (MCS) states entail powerful medical, ethical and legal debates. The recent description of the MCS highlights the crucial role of unexpected and well-documented recoveries of cognitive functions. Functional neuroimaging has provided new insights for assessing neuropathology and cerebral activity in these patients, providing information on the presence, degree, and location of any residual brain function in patients with PVS or MCS. We present a review on this topic, emphasizing the clinical and neuroimaging assessment of these states, with some of our recent results in this area. We conclude that the development of rehabilitation techniques for patients with PVS and others suffering long-lasting effects of brain injury is a crucial challenge for actual and future generations of neuroscientists.