Nasopharyngeal carcinoma (NPC) is rare in most parts of the world, but prevalent in south China. Recently, UBAP1 gene, which is located in the region of minimal heterozygosity deletion at 9p21.3～22.1 and down-expressed in NPC, has been cloned. The latest results suggest that the UBAP1 gene is the candidate tumor suppressor for NPC. Association study using 5 single nucleotide polymorphisms (SNPs) within UBAP1 gene by means of sequencing was performed in 105 unrelated case subjects and 183 control subjects which matched to the NPC cases on age, sex and residence. Occasionally, a novel SNP has been found, and been submitted to the dbSNP (accession number: ss4384147). Significant result was obtained for one SNP mark (rs1049557), which is resident at 3′ non-translation region of UBAP1 gene; the relative risk of this SNP mark is 1.64 (genotype GG) and 1.31(genotype CG). The result has proved again that UBAP1 gene may play a certain role in occurrence and development of nasopharyngeal carcinoma. The SNP mark rs1049557, considering it's residence, may influence on the expression of UBAP1 gene.