HER2 (c-erbB-2) has been suggested to be a prognostic factor in a variety of human cancers including breast, gastric and ovarian cancers. This study is therefore designed to identify changes of HER2 in nasopharyngeal carcinoma (NPC), an epithelia-derived malignancy with strong racial and geographic distribution. Interphase FISH and immunohistochemical (IHC) staining were used to analyze the gene copy number and protein expression of HER2 in 45 cases of NPC from Guangzhou, Southern China, an area with the highest incidence of NPC in the world. Our results, however, found no significant alterations in gene copy number for HER2, although IHC staining detected expression of HER2 oncoprotein in 33% of the 45 NPC tumors. No correlation was observed between HER2 expression and sex, age and clinical outcome of the patients, T stage, lymph node status, site and histopathological grading of the tumors. These results cast doubt on the value of HER2 as a prognostic factor for NPC.