Within the last few years a considerable number of molecular studies have provided evidence for the presence of Mycobacterium tuberculosis complex DNA in ancient skeletal and mummified material (1,7,9,18,27,28,34,38,41,47). Besides the mere evidence of M. tuberculosis complex DNA, initial information suggested a high frequency of tuberculosis in ancient populations (13), and we have recently provided evidence that this also holds true for pharaonic Egypt (47 (20), which is based on the variation of the direct-repeat (DR) region in M. tuberculosis complex members. Using this technique, differentiation up to a subspecies level is possible. Spoligotyping is widely used and accepted in medical microbiology for the initial genotyping of the M. tuberculosis complex at the population level. In addition, spoligotyping seems to be the most suitable method for analyzing ancient material, since usually only minute amounts of a significantly fragmented mycobacterial ancient DNA (aDNA) remains in the samples under investigation. Likewise, other recent methods, such as IS6110 restriction fragment length polymorphism (43), ligation-mediated PCR (31), and variable number of tandem repeat typing (24), require cell culture conditions or at least high-molecular-weight bacterial DNA and are therefore not applicable to ancient tissue material.In addition, spoligotyping seems to be suitable for investigating evolutionary aspects of human tuberculosis (36) and may clarify the origin and transmission of the disease in humans of various historical periods and populations (35). When its results are combined with other data, they can be used to construct phylogenetic trees reaching back to the beginning of the pathogenesis and spread of the disease in humans and animals (37).In this regard, there is still an open debate about the origins of tuberculosis in human and animal species. One previous hypothesis (5) suggests that M. bovis is the probable ancestor which was transmitted from cattle to humans during domestication. Other theories assume that an M. tuberculosis complex precursor evolved from M. africanum and that the present-day M. tuberculosis and M. bovis developed in parallel (39). This theory is supported by nucleotide sequence analyses of current M. tuberculosis isolates, revealing an absence of allelic variation. The evolutionary origin of M. tuberculosis was therefore suggested to be 15,000 to 20,000 years ago (39).In a recent paper, a new evolutionary scenario was presented based on the occurrence of several deletions in the genomes of the tubercle bacilli (4). These findings allow a differentiation of M. tuberculosis strains into modern and ancestral strains depending on the presence or absence of an M. tuberculosis-* Corresponding author. Mailing address: