The pooled OR of RUNX3 methylation in DCIS and NB or benign tumor under the fixed-effects model was 50.37 which indicated the frequency of RUNX3 hypermethylation in DCIS significantly increased compare to NB or benign tumor, the heterogeneity did not show significant difference among studies at Cochran's test, with low I2 index (0%), suggesting RUNX3 methylation is an early event during carcinogenesis which is consistent with the results of the original articles included in present study. The gene discussed is RUNX3; the disease is benign neoplasm.