Recently, epidemiology of M. tuberculosis have been performed by molecular techniques as a probe with the insertion sequence (IS) 6110. In the traditional study of tuberculosis epidemiology, information about social contact of persons and patient's illness history used to be an only relevant basis for elucidating transmission of tuberculosis infection. Therefore, it was very difficult to give a clear conclusion of whether isolates from different patients derived from a common source of infection or not. The subspecies typing of M. tuberculosis strains by IS6110 has become possible, based on the visualization of multiple loci of an insertion sequence (IS6110) that is a relatively stable gene fragment existing in a specific region of the genome. The variability of the number of copies and locations of this IS6110 in a genome is the basis that enables this technique to be used for the above purpose, which is a unique tool applicable to the analysis of M. tuberculosis. Generally, this technique, i.e., restriction fragment length polymorphism (RFLP) analysis, depends on the diversity of pattern of any polymorphic marker found in a genome of a strain. Among various markers so far developed and examined, IS6110 has been proved most appropriate for the purpose of typing strains of M. tuberculosis complex, especially in such circumstances as in Japan where isolated strains' RFLP patterns are similar each with others so that finer subtyping is needed. In this time, I would like to review the following topics based on the world literature of molecular epidemiology and the findings of our own that we have achieved during 1992 through 2001 in our Institute; (1) typing for the tracking of source of infection, (2) diffuse infection, (3) the presence of region-specific influential strains, (4) cross-contamination of strains in the laboratory, (5) the stability of IS6110, (6) phylogeny of tuberculosis (genotypes in Okinawa prefecture), and (7) the distinction between M. tuberculosis and M. bovis BCG, (8) computer-assisted patients management system. We also investigated the mode of transmission and risk factors of tuberculosis, based on the tuberculosis epidemiological data obtained in many parts of the world as well as the findings we gathered in our country from 1992 to 2001.