The inactivation of phosphatase and tensin homolog (PTEN) due to its CpG island hypermethylation has been observed in some types of tumors except nasopharyngeal carcinoma (NPC). In the present study, we focused on the aberrant methylation of PTEN CpG islands in NPC. The mRNA expression of PTEN was detected by quantitative PCR in 45 NPC and 22 non-tumor nasopharyngeal epithelial (NP) tissues. The methylation status of PTEN was examined by methylation-specific polymerase chain reaction and sequencing. The mRNA expression of PTEN in three NPC cell lines treated with 5-aza-2'-deoxycytidine (5-aza-dC) was also examined. PTEN was downregulated in both NPC tissues and NPC cell lines and a relatively higher methylation level of PTEN was found in NPC specimens (82.2%) relative to NP tissues (5.3%). The PTEN mRNA expression was restored in NPC cell lines by treatment with 5-aza-dC. These results first reveal an epigenetic alteration, aberrant methylation of PTEN, in NPC, which is probably an early event and may be regarded as a novel candidate biomarker for early stage of NPC detection and prevention.