The newly proposed variable-number tandem-repeat (VNTR) typing system, which includes a basic 15-locus set and a high-resolution 24-locus set (P. Supply et al., J. Clin. Microbiol. 44:4498-4510, 2006), demonstrated a high power for the discrimination of Mycobacterium tuberculosis isolates collected worldwide. To evaluate its ability to differentiate the Beijing genotype strains from the Beijing area in China, 72 isolates with typical Beijing or Beijing-like spacer oligonucleotide typing profiles were subjected to typing with the VNTR system (24 loci) and typing by restriction fragment polymorphism analysis with IS6110 (IS6110-RFLP). Compared to the "old" 12-locus VNTR typing method, use of the 15- and 24-locus systems had a dramatically improved power to discriminate the Beijing genotype strains. A subtle difference in the Hunter-Gaston discriminatory index (HGI) between the 15-locus and the 24-locus systems resulted from only one locus, Mtub29. However, the VNTR-based clusters could be further differentiated by IS6110-RFLP (HGI by IS6110 RFLP, 0.999), although in one case an IS6110 cluster was subdivided by the 15-locus VNTR system. In this sense, use of the newly proposed 15-locus VNTR system along with the Mtub29 locus can serve as a first-line typing method for the epidemiological study of M. tuberculosis isolates in Beijing, while secondary typing of clustered strains by IS6110-RFLP is still required.