The SOD1G93A transgenic mouse strain which carries a human mutant Cu/Zn superoxide dismutase transgene array is a widely studied model of amyotrophic lateral sclerosis. These mice have been used in many breeding experiments to look for interactions with other loci, including transgenic and gene targeted mutations. Therefore, we decided to map the site of the transgene insertion as this may affect the outcome of such breeding experiments. In a fluorescence in situ hybridization experiment we determined that the SOD1G93A transgene insertion site lies on distal mouse chromosome 12. This chromosome also carries the 'Legs at odd angles' locus, which is an entirely unrelated mutation in the dynein heavy chain gene that we have been studying. We have analysed data from a SOD1G93AxLoa cross and determined that the site of the transgene insertion lies proximal of the dynein heavy chain gene on mouse chromosome 12.