The species specificity of IS1607, a new Mycobacterium tuberculosis complex insertion sequence-related element, was investigated. IS1607 was present as a single copy in M. tuberculosis, M. bovis and M. bovis BCG strains. This sequence also existed in M. africanum and M. microti, but was not present in 69 strains of 19 atypical mycobacterial species analyzed by using polymerase chain reaction (PCR) or Southern hybridization assay. IS1607 appears to be specific for the M. tuberculosis complex.