Abstract: Objective To understand the polymorphism and proportion of variable number tandem repeat(VNTR) gene of Mycobacterium tuberculosis isolates from Inner Mongolia and the application of different VNTR loci for M. tuberculosis genotyping in Inner Mongolia.Methods The clinical M. tuberculosis strains isolated from confirmed tuberculosis patients, including the patients’ epidemiological and clinical information, were collected from Inner Mongolia Institute for Tuberculosis Control and Prevention and analyzed by the way of multi-Locus VNTR analysis(MLVA) with 22 VNTR loci. The polymorphism of different 22 VNTR loci were analyzed by the Hunter-Gaston Index with Bionumerics 5.0 software.Results Of all the 372 strains, 308 genotypes with 22 VNTR loci were detected, including 47 genotype clustering and 261 distinct genotypes. The clustering rate of genotype was 17.20%. In addition, the 22 loci had different polymorphisms, VNTR3820(HGDI 0.838) locus had highest discriminatory power, whereas MIRU23(HGDI 0.068) and MIRU27(HGDI 0.083) loci had lower discriminatory power. With the increase of the number of VNTR loci, the discriminatory power of VNTR analysis for M. tuberculosis strains was improved.Conclusion Gene polymorphism of clinical M. tuberculosis strains was observed in Inner Mongolia, and the different loci had distinct discriminatory power in VNTR analysis.