The paper aims to determine the main pathogen causing tuberculous lymphadenitis in infants. A total of 79 lymph node biopsies from 73 infants age 0-3 were conducted Mycobacterium tuberculosis (M. tuberculosis) identification, amplification of RD1, RD9 and RD10, and multiple-locus variable-number tandem repeat analysis (MLVA). The results showed that the main pathogen of tuberculous lymphadenitis in infants was bacillus Calmette-Guérin (BCG) (95.9%), followed by M. tuberculosis (4.1%). There were 4 genotypes including 3 independent genotypes (M. tuberculosis) and 1 genotype cluster analyzed by MLVA. The BCG isolated from clinical samples had no difference.