Nasopharyngeal carcinoma (NPC) is a malignant disease which had critically threatened human?蒺s health. It is very important to look for the biomarkers related to early diagnosis and prognosis of NPC. Using a series of large scale screening techniques from genomics, transcriptomics, proteomics and tissue microarray, combined with some international progress, a molecular marker system had been preliminarily constructed in different stages of NPC: (1) SPLUNC1, EBER-1, p16, p27, RASSF1A and CDH13, a group of molecular targets for the early diagnosis of NPC. (2) The class forecast model consisting of up-regulated RB1, STMN1, DSP and down-regulating SERPINB6, AGTRL1, SYTL2, the biomarkers to identify between normal nasopharyngeal epithelium and NPC. (3) NGX6, Ezrin, LTF, OPN, THY1 and Tiam-1, a group of candidate biomarkers forcasting the invasion and metastasis of NPC. (4) Cyclin D1，Survivin and HPA, a group of biomarkers related to the prognosis of NPC. (5) Bcl-2、EGFR and Ki67 proteins, a group of perfect candidate biomarkers for forecasting radiation sensitivity of NPC. (6) SAA and cox-2, the candidate biomarkers monitoring NPC recurrence. (7) The changes of six SNP from BRD7, NGX6, NOR1 and UBAP1, a group of the inheritance susceptibility risk factors. (8) Constructing a biomarker system of different clinical stages of NPC composed of 139 genes. These biomarkers based on screening with large amounts of samples lay an important foundation for molecular typing research of NPC.