Molecular typing is now widely used in mycobacteriology as a significant addition to conventional epidemiological studies. Several methods are available that differ with respect to their discriminating power and to the genetic marker used. Restriction fragment length polymorphism (RFLP) done using the IS6110 insertion sequence has been widely used for typing Mycobacterium tuberculosis. More recently, short repetitive DNA sequences have been used as RFLP markers, as well as for other typing methods involving gene amplification. One of these methods, the inter-direct repeat (DR)-based spoligotyping method, is rapid, directly applicable to clinical specimens, and highly discriminating.