Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC).Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treatment and provide epidemiological information. In this study, a multiplex real-time PCR diagnostics assay using novel molecular targets was designed to identify the MTC while simultaneously differentiating between M. tuberculosis and M. canettii. The lepA gene was targeted for the detection of members of the MTC, the wbbl1 gene was used for the differentiation of M. tuberculosis and M. canettii from the remainder of the complex, and a unique region of the M. canettii genome, a possible novel region of difference (RD), was targeted for the specific identification of M. canettii. The multiplex real-time PCR assay was tested using 125 bacterial strains (64 MTC isolates, 44 nontuberculosis mycobacteria [NTM], and 17 other bacteria). The assay was determined to be 100% specific for the mycobacteria tested. Limits of detection of 2.2, 2.17, and 0.73 cell equivalents were determined for M. tuberculosis/M. canettii, the MTC, and M. canettii, respectively, using probit regression analysis. Further validation of this diagnostics assay, using clinical samples, should demonstrate its potential for the rapid, accurate, and sensitive diagnosis of TB caused by M. tuberculosis, M. canettii, and the other members of the MTC.Tuberculosis (TB) is the leading cause of death worldwide from an infectious agent (13), with the WHO estimating that one-third of the global population is infected with Mycobacterium tuberculosis. In a global report from the WHO (2009), it was estimated that there were 9.27 million cases of TB in 2007, with 2 million associated deaths (41a). TB in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). The eight closely related species of the MTC have a wide range of natural hosts, including human hosts (M. tuberculosis, M. africanum, M. canettii), bovine hosts (M. bovis), caprine hosts (M. caprae), rodent hosts (M. microti), and pinniped hosts (M. pinnipedii), along with the attenuated M. bovis strain BCG (Bacillus Calmette-Guérin), the commonly used vaccine strain. While there are a number of natural hosts, each species of the MTC has been implicated in human infection (6,20).Traditionally, diagnosis of TB relies on smear microscopy and culture techniques in combination with a battery of biochemical tests which are time-consuming and labor-intensive and which often yield unreliable results (18). Nucleic acid diagnostic (NAD) techniques, in particular, real-time PCR, offer rapid, reliable, and highly sensitive alternative tools for the detection of many infectious agents (25, 42). Advances in real-time PCR, such as the availability of multiple fluorophores, along with the development of nonfluorescent quenchers, have facilitated multiplexing, allowing the simultaneous detection and differentiat...