Squamous cell carcinoma (SCC) of the head and neck remains a major health problem worldwide. Recent advances in cell biology suggest that cancer results from the accumulation of specific genetic mutations, many of which have now been identified. These mutations can cause the activation of genes that promote cellular proliferation or inhibit cell death (oncogenes), or they may inactivate genes that inhibit proliferation or promote cell death (tumour suppressor genes). Although there is no known set sequence of events leading to the formation of SCC of the head and neck, there is evidence that many of the genomic mutations implicated in other forms of cancer have an aetiological role in these tumours. Certain viruses, notably Epstein-Barr virus and some types of human papillomaviruses, are causally related to some head and neck cancers. There is now the prospect of using molecular markers to achieve earlier diagnosis and to aid in the prediction of both tumour behaviour and likely responses to particular treatment modalities.