As members of adhesion molecule families, CD44 transmembrane glycoproteins have been originally thought to be essential for the formation of multicellular organisms and soon recognised to be able to initiate metastatic spread of tumour cells. To investigate the association between CD44 polymorphisms and nasopharyngeal carcinoma (NPC), we carried out a two-stage case–control study in 906 patients and 943 healthy controls in Eastern populations. Five single nucleotide polymorphisms of CD44 (rs10836347C>T, rs13347C>T, rs1425802A>G, rs11821102G>A and rs713330T>C) with proper frequency were selected from the HapMap database and genotyped with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Compared with the most common rs13347CC genotype, CT+TT genotypes significantly increased individuals’ susceptibility to NPC (odds ratio = 2.58, 95% confidence interval = 2.13–3.13). Furthermore, our transient transfection focusing on reporter gene expression modulated by CD44 3′UTR demonstrated that the presence of an rs13347T allele led to greater transcriptional activity than the C allele. Similarly, more CD44 expression was shown in rs13347T carriers than C carriers in our western blotting results. All these findings suggest that CD44 rs13347C>T polymorphism may affect NPC development by improving CD44 expression.