In this study, we have shown that the alteration of methylation ratio at all single CpG sites of the target fragment of TAP1,LMP7 and ERp57 genes was positively correlated, and the methylation level of these CpG sites was significantly higher in CIN or CSCC cases compared with normal. The gene discussed is PDIA3; the disease is cervical squamous intraepithelial neoplasia.