The progressive loss of colour in the hair of grey horses is controlled by a dominantly inherited allele at the Grey locus (GG). In this study, two paternal Quarter Horse (QH) families segregating for the GG allele were genotyped with a set of 101 microsatellite markers spanning the 31 autosomes and the X chromosome. This genome scan demonstrated linkage of Grey to COR018 (RF=0.02, LOD=12.04) on horse chromosome 25 (ECA25). Further chromosome-specific analysis of seven total QH families confirmed the linkage of Grey to a group of ECA25 markers and the map order of NVHEQ43-(0.24)-UCDEQ405-(0.09)-COR080-(0.05)-GREY-(0.14)-UCDEQ464 was produced. Although G was found to be linked to TXN and COR018 in the chromosome-specific analysis, the data were not sufficiently informative to place either marker on our ECA25 map with significant LODs. Our results excluded the equine tyrosinase related protein 1 (TYRP1) and melanocyte protein 17 (Pmel17) genes as possible candidates for the grey phenotype in horses.