Alpha-chloralose is commonly used during animal fMRI studies for anesthesia, however, recovery of animals is difficult, limiting experimental design. The use of a less invasive anesthetic would enable chronic experiments. The present study compares functional activity in the spinal cord of the alpha-chloralose and halothane-anesthetized rat. Functional MRI of the rat cervical spinal cord was performed on 6 alpha-chloralose and 6 halothane-anesthetized rats in a Bruker 7 T MR system during electrical stimulation of the right forepaw. Following imaging, four animals from each group were perfused and spinal cords removed for immunohistochemical analysis. Areas of c-fosexpression were identified with immunofluorescent labeling to confirm the presence of neuronal activity. Functional activity and c-fosexpression were observed predominantly between the fifth and seventh cervical spinal cord segments. Areas of fMRI activation in the spinal cord correspond well with spinal cord physiology. Areas of c-fosexpression confirmed that neuronal activity was present in the regions of fMRI activity. The regions and amount of fMRI activity observed were similar for both anesthetics. Functional magnetic resonance imaging of the spinal cord can be achieved using both alpha-chloralose and halothane anesthesia in rats. We therefore suggest that halothane may be used as an anesthetic agent for chronic fMRI studies of the spinal cord.