Abstract Objective Genome-wide association study (GWAS) in Icelanders identified HLA class II sequence variants on chromosome 6p21 as tuberculosis (TB) susceptibility loci. To evaluate the role of these loci in other populations with different ancestry, we conducted a case-control study in Chinese population. Methods We genotyped two genetic variants (rs9272461 and rs9271300) on the reported chromosome 6p21 in 739 pulmonary tuberculosis (PTB) cases and 749 healthy controls from Chinese Han population using TaqMan allelic discrimination assay. Logistic regression was applied to evaluate the association between genetic variants and PTB risk and to estimate corresponding odds ratios (ORs) and 95% confidence intervals (95%CIs). Results We found that rs9272461 was significantly associated with the risk of PTB in various genetic models (dominant OR = 0.75, 95%CI: 0.61–0.92; recessive OR = 0.64, 95%CI: 0.46–0.90, and additive OR = 0.78, 95%CI: 0.67–0.90). Moreover, in the stratified analysis in additive model, the association was also significant in the old (age ≥ 48 years) (OR = 0.76, 95%CI: 0.62–0.93; P =.008), men (OR = 0.71, 95%CI: 0.59–0.85; P <.001), and new PTB cases (OR = 0.76, 95%CI: 0.65–0.90; P =.001). The association results were similar between the microbiologically negative (OR = 0.78, 95%CI: 0.64–0.94; P =.008) and positive cases (OR = 0.77, 95%CI: 0.64–0.93; P =.008). We did not observe significant association for rs9271300 neither in the overall analysis (additive model: OR = 0.98, 95%CI: 0.85–1.13; P =.776) nor in the stratified analysis. Conclusions Our findings indicate that the HLA class II locus also affects the susceptibility to PTB in Chinese population. Further validation studies and function experiments are required to confirm the roles of the discovered variant. Highlights • An HLA class II sequence variant rs9272461 was associated with the risk of PTB in Chinese population. • The HLA class II locus could influence the susceptibility to PTB in the old, men and new cases. • The HLA class II locus showed similar associations with both microbiologically negative and positive PTB. [ABSTRACT FROM AUTHOR]