We performed a stratification analysis by histological type, which is lacking in most previous studies, and found that the MTHFR 677 CT genotype was associated with a significantly decreased risk for lung squamous cell carcinoma (OR = 0.78, 95%CI = 0.64-0.96), supporting the potential effect of MTHFR C677T polymorphism on lung squamous cell carcinoma. Here, MTHFR is linked to squamous cell lung carcinoma.