Polymorphisms in some immunomodulatory genes are associated with susceptibility to non-small cell lung cancer (NSCLC). A total of 1,193 NSCLC patients and 1,056 healthy controls were recruited in this study to explore the association between polymorphisms of PD-1, HMGB1, and LFA-1 and the risk of NSCLC. Three related polymorphisms, PD-1 rs36084323, HMGB1 rs1412125 and LFA-1 rs2230433, were screened out by SNPscan™. The HMGB1 rs1412125 (T > C) genotype increased NSCLC susceptibility (CC vs TT: P = 0.006; CC vs TT + TC: P = 0.007), while LFA-1 rs2230433 G > C and PD-1 rs36084323 T > C genotypes were not associated with increased NSCLC risk. Further stratified analysis revealed that the HMGB1 rs1412125 T > C genotype increases NSCLC risk in men (homozygote: OR = 2.20, P = 0.004; dominance: OR = 1.29, P = 0.044; recessive: OR = 2.05, P = 0.008) and in smokers (homozygous: OR = 2.25, P = 0.030; dominance: OR = 1.48, P = 0.026). In summary, the HMGB1 rs1412125 T > C polymorphism increases NSCLC susceptibility.