Rat remains a major biomedical model system for common, complex diseases. The rat continues to gain importance as a model system with the completion of its full genomic sequence. While the genomic sequence has generated much interest, only 3 complete sequences of the rat mitochondria exist. Therefore, to increase the knowledge of the rat genome, the entire mitochondrial genomes (16,307-16,315bp) from ten inbred rat strains (that are standard laboratory models around the world) and two wild rat strains were sequenced. We observed a total of 195 polymorphisms, 32 of which created an amino acid change (non-synonymous substitutions) in twelve of the thirteen protein coding genes within the mitochondrial genome. There were eleven single nucleotide polymorphisms within the transfer RNA (tRNA) genes, six in the 12S ribosomal RNA (rRNA) and 12 in the 16S rRNA including 3 insertions/deletions. We found fourteen single nucleotide polymorphisms and two insertion/deletion polymorphisms in the D-loop. The inbred rat strains cluster phylogenetically into three distinct groups. The wild rat from Tokyo grouped closely with five inbred strains in the phylogeny, while the wild rat from Milwaukee was not closely related to any inbred strain. These data will enable investigators to rapidly assess the potential impact of the mitochondria in these rats on the physiology and the pathophysiology of phenotypes studied in these strains. Moreover, these data provide information that may be useful as new animal models, which result in novel combinations of nuclear and mitochondrial genomes, are developed.