Certain brain-computer interface (BCI) methods use intrinsic signals from the motor cortex to control neuroprosthetic devices. The organization of the motor pathways in those populations likely to use neuroprosthetic devices, therefore, needs to be determined; there is evidence that following disease or injury the representation of the body in the motor cortex may change. In this study, functional MRI measures of somatotopy following spinal cord injury (SCI) showed evidence of changes in limb representations in the motor cortex. Subjects with chronic SCI had unusual cortical patterns of activity when attempting to move limbs below their injury; amputees showed a more normal somatotopy. The functional reorganization may affect optimal implanted electrode placements for invasive BCI methods for these different populations.