While acute pain serves as a protective mechanism designed to warn an individual of potential or actual damaging stimuli, chronic pain provides no benefit and is now considered a disease in its own right. Since the advent of human brain imaging techniques, many investigations that have explored the central representation of acute and chronic pain have focused on changes in higher order brain regions. In contrast, far fewer have explored brainstem and spinal cord function, mainly due to significant technical difficulties. In this review, we present some of the recent human brain imaging studies that have specifically explored brainstem and spinal cord function during acute noxious stimuli and in individuals with chronic pain. We focus particularly on investigations that explore changes in areas that receive nociceptor afferents and compare humans and experimental animal data in an attempt to describe both microscopic and macroscopic changes associated with acute and chronic pain.