Abstract: Objective To evaluate the clinical value of multi-locus polymerase chain reaction (PCR) for identifying Mycobacterium tuberculosis complex isolated in children. Methods The isolates were collected and were first determined by PNB/TCH medium. 7-point PCR sites including 16SrRNA, Rv0577, IS1561, Rv1510, Rv1970, Rv3877/8 and Rv3120, and 4-point PCR sites including ropB, RD1, RD8 (present), RD8 (deleted) were used to amplify them by PCR. Results Total of 204 isolates were collected, in which 199 were Mycobacterium tuberculosis, 3 were Mycobacterium bovis, and 2 were non-tuberculous mycobacteria by the PNB/TCH method. 4-point PCR analysis showed that 196 were Mycobacterium tuberculosis, 2 were Mycobacterium bovis, 3 were BCG species and 3 were non-tuberculous mycobacteria. 7-point PCR analysis showed that 191 were Mycobacterium tuberculosis, 2 were Mycobacterium bovis, 3 were BCG species, 4 were African Mycobacterium type I, 1 was Mycobacterium caprae, 1 was Mycobacterium microti and 2 were non-tuberculous mycobacteria. Conclusion Compared with the conventional method, the PCR identification in 4-point PCR method and 7-point PCR method could rapidly identify the BCG among the complex group in children tuberculosis. 7-point PCR method was able to identify all the subspecies of Mycobacterium, except Africa Mycobacterium. 4-point PCR method would be more rapid and easier in the identification of BCG strains.