Molecular typing methods based on polymorphisms in single nucleotides and short tandem repeat motifs have been developed as epidemiological typing tools for Mycobacterium leprae. We have used a variable number tandem repeat method based on three variable loci to identify strain variation in archaeological cases of lepromatous leprosy. The panel of polymorphic loci used revealed unique profiles in five cases of leprosy, including those with identical SNP type and subtype. These were also different from profiles of three previously studied lepromatous skeletons. Whilst examination with SNP typing provides evidence for disease origins, dissemination and phylogeny, tandem repeat typing may be useful for studying cases from within a defined area or community where SNP types may be identical due to geographical constraints. We envisage the technique may be useful in studying contemporaneous burials such as those associated with leprosaria and will prove invaluable in authentication of ancient DNA analyses.