Objective：To investigate the relationship between ATG4A gene rs807185（T/A），ATG16L1 gene rs2241880（A/G） polymor－phism and the susceptibility to pulmonary tuberculosis（PTB） in the Southwestern Chinese population. Methods：The single nucleotide polymorphism（SNP） of the ATG4A gene rs807185 and ATG16L1 gene rs2241880 were genotyped by polymerase chain reaction-re－striction fragment length polymorphism（PCR-RFLP） in 218 cases versus 248 controls. Logistic regression was used to analyze the correlation between the site and the susceptibility to PTB. Results：Frequencies of A allele（OR=0.69，95%CI=0.51 to 0.92，P=0.012），AT genotype（OR=0.53，95%CI=0.30 to 0.92，P=0.025），and AA+AT vs. TT（OR=0.62，95%CI=0.42 to 0.92，P=0.017） were reduced significantly in cases than in controls. In female respondents，aforementioned indices did the same. The frequencies distribution of geno－type，allele and dominant/recessive model in rs2241880 site had no significant difference（P >0.05） in cases and controls. Conclusion：Genetic variant in ATG4A gene（rs807185） are associated with pulmonary tuberculosis susceptibility in a Southwestern Chinese pop－ulation. However，the SNP of ATG16L1 rs2241880 might not be associated with the susceptibility to PTB.