We have recently reported that inactivation of the p16 gene by mutation and deletion is common in nasopharyngeal carcinoma (NPC). The present study demonstrates that hypermethylation of the 5' CpG island can serve as an alternative mechanism for inactivation of the p16 gene in this tumor. Using Southern blotting analysis and multiplex PCR, aberrant methylation of the 5' CpG island of the p16 gene was found in a NPC xenograft (xeno-666) and 6 (22%) of 27 primary tumors, but not in normal tissues of the nasopharynx. In the NPC xenograft (xeno-666) and its newly derived cell line (cell-666), both showing hypermethylation of the p16 gene, no p16 gene expression was found. After treatment with 5-aza-2'-deoxycytidine, reexpression of the p16 gene was detected in the cell line cell-666. These findings suggest that aberrant methylation of the 5' CpG island may participate in the transcriptional inactivation of the p16 gene in NPC. The present results further support that the p16 gene is the critical target on chromosome 9p21 for inactivation during the development of this disease.