Inconsistent results are often found regarding the risk of genetic variants in lung cancer association studies. To alleviate these conflicts, we performed a large-scale meta-analysis to evaluate the effect of variants on lung cancer in East Asian population (Han Chinese, Japanese, and Korean). Forty-three genetic variants with data from at least three independent case-control studies were under investigation of which two variants (rs1800734 in hMLH1, rs2273953-rs1801173 bi-marker in P73) were first meta-analyzed in East Asians. We found that three variants in CYP1A1, GSTM1, and XRCC1 showed consistently significant associations with lung cancer in mixed analysis and stratified analysis, and several variants showed diverse effects interacting with different environmental factors in stratified analysis. Our study presents a comprehensive and systematic analysis of lung cancer association studies in East Asians and confirms the effect of three variants in lung cancer risk. Additionally, result from stratified analysis suggests the importance of inclusion of environmental factors, such as smoking and tumor histology, in the analysis.