Spinal ventral root avulsion leads to an inflammatory response around lesioned motoneurons and the subsequent degeneration of a large proportion of the neurons. We demonstrate here differences in the regulation of cytokine mRNAs, microglia/macrophage activation, MHC expression and nerve cell survival in the two inbred rat strains DA and ACI. These strains have similar major MHC haplotypes, but differ in their non-MHC background genes. T cells were rare in the lesioned segments and depletion of T cells did not affect the response. Thus, non-MHC gene(s) regulate the inflammation and neuron death after nerve trauma by mechanisms not involving antigen-specific immune responses.