The detection rate of methylated SEPTIN9, RASSF1A, and H4C6 in nasopharyngeal swabs of patients with newly diagnosed NPC was 88.2%, 92.9% and 71.8%, respectively, while it reduced to 54.3%, 42.9% and 45.7% in blood plasma. Here, SEPTIN9 is linked to nasopharyngeal carcinoma.