The nuclear insertions of mitochondrial DNA (Numts), which originate from the integration of nuclear DNA by mtDNA, are found as molecular fossils in the nuclear genomes of various eukaryotes. Because integrated Numts tend to have a high sequence similarity to genuine organellar mtDNA sequences, inadvertent amplification of Numts can be a nuisance in studies of mtDNA variation. With the availability of the complete domestic horse genome sequence, we present the first comprehensive analysis of genome-wide distribution and frequency of Numts in the nuclear genome of domestic horse ( Equus caballus
). In the present paper, we detected 200 Numts ranging between 29 and 3 727 bp in size, which collectively representing only 0.002154% of the nuclear genome. Furthermore, ten of these segments were found to be longer than 800 bp. The absence of Numts in mitochondrial control region suggested that it would not influence the analysis of horse population genetics studies relating to this region. We also found that during horse evolution, Chromosomes 1 and 27 have been more susceptible to integration by Numts. The results in this study may provide valuable information for future mtDNA studies in Equidae species, including its use as a tool for avoiding Numt contaminations that may result in inauthentic results of experimentation.