In the stratified analysis by method, significantly increased breast cancer risk was associated with APC methylation by both QMSP method (OR = 3.11, 95% CI = 1.72–5.62, P = 0.0002) and MSP method (OR = 13.38, 95% CI = 4.34–41.25, P < 0.00001). This evidence concerns the gene APC and breast cancer.