In order to further examine expression of cDNA fragments isolated by cDNA representational difference analysis(cDNA RDA) in nasopharyngeal carcinoma(NPC) biopsies and to clone those deregulated genes associated with NPC, RT-PCR and Northern blot were used to identify the differentially expressed cDNA fragments in NPC biopsies and confirm the transcript length of those genes, then a full-length cDNA sequences was cloned and its product was analyzed by bioinformatics. The results showed that AF091521, AF091520, AF152605 and AF091517 cDNA sequences had distinct expression difference between primary cultural normal nasopharyngeal epithelial cell and NPC biopsies, and AF091521, AF091517 genes all had two transcripts whose sizes were 1.5, 2.3 and 1.1, 1.4 kb respectively, while AF091520 and AF152605 gene expressed one transcript only, respectively, whose sizes were 1.6 and 2.2 kb. An AF091517 EST gene, named as NAG11, (GenBank accession number AF170307) was isolated by sequencing one EST clone, which encoded a transmembrane protein of 88 amino acid including three protein ATP-binding regions, two protein kinase C phosphorylation sites and two N-myristoylation sites. So it is further demonstrated that NPC is a disease with multiple gene alterations NAG11 gene is a candidate of putative tumor suppressor genes associated with NPC, whose down-expression may be involved in the development of NPC and NAG11 gene product may play a role in the transmembrane transport of ATP.