The invention belongs to the field of genetic engineering and oncology, and discloses a low-frequency high-penetrance genetic marker associated with the auxiliary diagnosis of primary lung carcinoma and applications of the marker. The marker is a combination of 35 genetic loci such as rs1131897, rs1133833, rs115019901, rs117855259, rs118154190, rs141059768, rs141350740, rs142881943, rs145529151, rs145638335, rs145940981, rs150279473, rs150695913, rs151223396, rs185832840 and rs188159138. The marker can be used for preparing kits for the auxiliary diagnosis of primary lung carcinoma.