Stratification analysis showed that ethnicity, disease type, and quality score might be the factors of heterogeneity across all studies of association between FAS −670 A/G polymorphism and autoimmune diseases risk, and quality score may be the factor of heterogeneity across all studies of association between FAS −1377 G/A polymorphism and autoimmune diseases risk. The gene discussed is FAS; the disease is autoimmune disease.