Progress in management of critically ill neurological patients has led to improved survival rates. However, severe residual neurological impairment, such as persistent coma, occurs in some survivors. This raises concerns about whether it is ethically appropriate to apply aggressive care routinely, which is also associated with burdensome long-term management costs. Adapting the management approach based on long-term neurological prognosis represents a major challenge to intensive care. Magnetic resonance imaging (MRI) can show brain lesions that are not visible by computed tomography, including early cytotoxic oedema after ischaemic stroke, diffuse axonal injury after traumatic brain injury and cortical laminar necrosis after cardiac arrest. Thus, MRI increases the accuracy of neurological diagnosis in critically ill patients. In addition, there is some evidence that MRI may have potential in terms of predicting outcome. Following a brief description of the sequences used, this review focuses on the prognostic value of MRI in patients with traumatic brain injury, anoxic/hypoxic encephalopathy and stroke. Finally, the roles played by the main anatomical structures involved in arousal and awareness are discussed and avenues for future research suggested.