Functional magnetic resonance imaging (fMRI) is a powerful technique for the functional investigation of the brain and spinal cord. Although some progress has been recently made, many issues still need to be solved for fMRI to be used for clinical and preclinical investigations of the spinal cord. Currently, we are developing new strategies to apply fMRI on the spinal cord of healthy subjects and in patients. These strategies include acquisition and data analysis protocols for the reduction of physiological noise (due to cardiac pulse and respiration), which is the main reason for the low signal-to-noise ratio observed in functional series of the spinal cord.