A large number of molecular pathways have been implicated in the degeneration of axotomized motoneurons. We previously have demonstrated substantial differences in the survival rate of axotomized motoneurons across different rat strains. Identification of genetic differences underlying such naturally occurring strain differences is a powerful approach, also known as forward genetics, to gain knowledge of mechanisms relevant for complex diseases, like injury-induced neurodegeneration. Overlapping congenic rat strains were used to fine map a gene region on rat chromosome eight previously shown to regulate motoneuron survival after ventral root avulsion. The smallest genetic fragment, R5, contains 35 genes and displays a highly significant regulatory effect on motoneuron survival. Furthermore, expression profiling in a F2(DAxPVG) intercross demonstrates one single cis-regulated gene within the R5 fragment; Gsta4, encoding glutathione S-transferase alpha-4. Confirmation with real-time PCR shows higher Gsta4 expression in PVG compared with DA both in naïve animals and at several time points after injury. Immunolabeling with a custom made rat Gsta4 antibody demonstrates a neuronal staining pattern, with a strong cytoplasmic labeling of motoneurons. These results demonstrate and map naturally occurring genetic differences in the expression of Gsta4 is associated both with a highly significant increase in the survival of axotomized motoneurons and with a trans-regulation of several molecular pathways involved in neurodegenerative processes. This adds to a large body of evidence implicating lipid peroxidation as an important pathway for neurodegeneration.