The aim of this study was To characterize Mycobacterium tuberculosis isolates by MIRU-VNTR typing and IS 6110 – RFLP and to compare the efficiency of MIRU-VNTR typing and IS 6110 – RFLP in discriminating Mycobacterium tuberculosis isolates. In Mycobacterium genome a large number of insertional and repetitive elements have been identified. In the genome of Mycobacterium tuberculosis insertation sequence IS 6110 is present.. In Mycobacterium tuberculosis, 41 mini satellites like structure have been identified. They are specific class of variable number of tandem repeats at different loci varies between strain. MIRU-VNTR, is a widely accepted technique for strain typing of Mycobacterium tuberculosis. Analysis of fingerprinting of M.tuberculosis strains showed the presence of both low (5%) and multiple (95%) IS6110 copy number strains. After genotyping the same isolates by MIRU-VNTR typing it is showed that MIRU-VNTR typing is more sensitive than IS 6110-RFLP. As MIRU-VNTR typing is less time taking, less DNA are required and Bands obtained are clear so easy to interpretate.