The ability to reproducibly discriminate Mycobacterium bovis isolates and trace their transmission has the potential to clarify sources of infection and major routes of transmission for bovine tuberculosis (TB). A PCR-based genotyping assay has been developed to discriminate between strains of M bovis by examining multiple sites in its genome that consist of variable numbers of tandem repeats (VNTRs). The discriminatory power and reproducibility of this VNTR typing has been compared with that of the established PCR-based spoligotyping technique by using a panel of 461 isolates of M bovis prevalent in Northern Ireland. The VNTR assay discriminated 40 different profiles, the most prevalent of which constituted 21 per cent of the total, compared with 14 profiles discriminated by spoligotyping, the most prevalent of which constituted 65 per cent. No significant differences were observed between the prevalences of the VNTR profiles in the years from 1999 to 2003. A preliminary evaluation indicated that most genotypes predominated in particular areas of the country. This VTNR typing assay was found to be highly discriminating, with the performance characteristics to support its systematic application to the molecular epidemiology of bovine TB.