The CYP2A6 rs1801272 polymorphism was significantly associated with a decreased lung cancer risk in squamous cell carcinoma cases (OR = 0.47, 95%CI = 0.27–0.81, ptrend = 0.007; test for heterogeneity by histology: pheterog = 0.045). Here, CYP2A6 is linked to squamous cell carcinoma.