Nasopharyngeal carcinoma (NPC) is a rare malignancy tumor in most parts of the world, while with high incidence rate in the south of China. NOR1, a NPC down-regulated gene, was newly-cloned using cDNA micro-array. NOR1 gene has an oxidored-nitro domain predicted by bioinformatics. The latest results suggest that the NOR1 gene may participate in the metabolism of chemical carcinogen such as nitrosamine in vivo. Genotype of coding region single nucleotide polymorphisms (cSNPs) in NOR1 gene were performed by sequencing in 144 unrelated NPC subjects and 144 control subjects which matched in age, sex and residence. Association analysis suggests that there is linkage disequilibrium between the 2 cSNPs, both of them associated with NPC. And the relative risk of 2 cSNPs and their haplotypes were 1.36, 1.64 and 1.37 respectively. Both of the two SNPs could change the sequence of NOR1 protein, which might influence it's structure and function. The results indicated that the SNPs in NOR1 gene may play a certain role in carcinogenesis and development of NPC.