Inflammation is a common characteristic of spinal cord injury. The nature of this response, whether it is beneficial or detrimental, has been the subject of debate. It has been reported that susceptibility to autoimmunity is correlated with increased functional impairment following spinal cord injury. As the ability to mount an autoimmune response has most consistently been associated with certain haplotypes of the major histocompatibility complex (MHC), we analysed the possible effects of the MHC haplotype on functional impairment and recovery following spinal cord injury. A contusion injury was induced in experimental autoimmune encephalomyelitis-susceptible and -resistant rats [Dark Agouti, Lewis and Piebald Viral Glaxo (PVG), respectively]. We found that locomotion recovered significantly better in Dark Agouti rats compared with PVG and Lewis rats but an F2 intercross (PVG × PVG-RT1av1) excluded the possibility that this difference was MHC haplotype-dependent. Thus, we conclude that recovery following spinal cord injury is subject to considerable genetic heterogeneity that is not coupled to the MHC haplotype region. Continued research of genetic variants regulating recovery following spinal cord injury is warranted.