In this article, we consider the tools of molecular genetics and strategies that have, or likely will have, an impact in otolaryngology, either as diagnostic tools or as strategies, with more far-reaching applications in tumour therapy, relapse monitoring, and ultimately, approaches to tumour prevention. Nasopharyngeal carcinoma (NPC) is closely associated with Epstein-Barr virus (EBV). Detection of the virus following gene amplification by the polymerase chain reaction (PCR) can provide a diagnostic tumour marker, both in primary and metastatic sites. NPC can be considered as a model disease on which molecular genetics is and likely will be of considerable impact. NPC is characterized by the presence of a genetically stable, viral agent of proven oncogenicity. The presence of attractive experimental systems for the study of EBV-associated tumours and their accessibility may combined with new molecular approaches towards diagnostic and, eventually, therapeutic improvements in the treatment of this clinically ominous malignancy.