The distribution of proteins in the cerebral cortex of a seizure-sensitive (SS) strain of gerbil and its seizure-resistant (SR) counterpart was profiled using two-dimensional gel electrophoresis. A series of proteins of similar molecular weight (around 83 kDa) showed small but consistent differences in their isoelectric point (pI) with indistinguishable profiles of distribution between the two strains. Amino acid sequences of peptides produced by limited proteolysis of each protein in the spots from the strains were identical or highly homologous to those of mitofilin, a mitochondrial inner membrane protein (IMMT) in humans. Analysis of cDNA sequences revealed the proteins of these spots to be gerbil mitofilin-like proteins (gIMMT), with a few base substitutions between SS and SR strains, in particular within a region near a putative transmembrane domain that is highly conserved in humans and gerbils. The amino acid at the site was acidic, Glu in humans and Asp in the strain SR of gerbil and a neutral, Asn in strain SS. In addition to these base substitutions, production of multiple species of mRNA for gIMMT by alternative splicing was observed.