In contrast to a substantial inventory of mitochondrial d-loop sequences from the West European part of the range of the western house mouse Mus musculus domesticus, there are few such data from close to the Middle Eastern origin of the subspecies. This paper attempts to rectify this situation, with details of d-loop sequences of 92 mice from 45 localities in Turkey, adding to the six mice from three localities previously studied from that country. The molecular data were found to be consistent with Turkey being close to the site of origin of M. m. domesticus. The 54 Turkish haplotypes were distributed throughout a phylogenetic tree incorporating representative sequences described previously, and there was high nucleotide diversity among the Turkish mice. There was weak genetic structure in Turkey, although haplotypes of the ‘Main Turkish Clade’, while common over much of Turkey, were absent from Southern Anatolia. Haplotypes of the Main Turkish Clade were also found in western Europe and it is believed that they derived from Turkey, which thus represents one of the source areas for the westwards expansion of M. m. domesticus. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84, 473–485.