The lung cancer mortality rate in Xuan Wei is among the highest in China and has been causally attributed to high exposure to indoor smoky coal emissions, which contain high levels of PAHs and can lead to modified bases. We studied genetic polymorphisms in four DNA base excision repair genes in a population-based case-control study in Xuan Wei with 122 lung cancer cases and 122 controls. Homozygous carriers of the APEX1 148Glu variant had an increased risk (OR, 2.13; 95% CI, 0.96-4.74), whereas persons with the XRCC1 399Gln allele had a decreased risk (OR, 0.60; 95% CI, 0.35-1.02) of lung cancer compared with wild-type carriers. Subjects with both at-risk genotypes (APEX1 Glu148Glu and XRCC1 Arg399Arg) had a higher risk of lung cancer (OR: 3.34; 95% CI: 1.16-9.67). We found genetic variants in APEX1 and XRCC1 may alter the risk of lung cancer in a special population in China.