At least five dinucleotide (CA)n microsatellite repeat arrays have been assigned to the bovine Y-chromosome, with one marker (INRA124) shown to be polymorphic. We describe here the assessment of a panel of four Y-specific microsatellite markers for polymorphism in a range of cattle and related species. It was possible to amplify all the markers in the animals sampled and all showed variation. Three of the microsatellite loci (INRA124, INRA189 and BM861) displayed putative taurine- and zebu-specific alleles which can be useful indicators of male-mediated gene flow in hybrid populations. In the future these microsatellites, in combination with other Y-specific markers should provide a high-resolution Y haplotype system for evolutionary studies in both domesticated cattle and other related species.