The consequences of spinal cord injury (SCI) have considerable effects on motor function, typically resulting in functional impairment. Pathological changes have been studied at the site of trauma, rostrocaudally within the cord, and in the periphery. Few studies, however, have investigated the consequences of SCI at the cortical level. Magnetic resonance imaging (MRI) was used to explore the morphological changes in the grey and white matter within the primary motor (M1) cortex of individuals with cervical SCI. The "precentral knob," a landmark of M1 cortex dedicated to hand function, was selected for regionally specific measurements of change. Thirty-one hemispheres of SCI subjects and 28 hemispheres of control subjects were compared using a manual measurement after the images were segmented into grey matter, white matter, and cerebral spinal fluid (CSF). No significant differences in grey matter area measured at the precentral knob were found with the manual approach. An automated voxel-based morphometric analysis was also performed and demonstrated no significant differences in grey or white matter volume within an M1 region of interest. These data suggest that there is no gross anatomical change within M1 following cervical SCI. Our previously reported findings of reorganization of cortical motor output maps following SCI therefore likely result from changes in functional organization rather than anatomical changes.