The human p63 gene encodes a series of protein isoforms that differ in their N- and/or C-terminal sequences and possess widely varying activities in promoting or repressing p53-related functions and in regulating the proliferation and differentiation of epithelial cells. To gain further information on the role of p63 expression in human tumours, we used quantitative real-time RT-PCR to study individual p63 isoforms in squamous cell carcinomas of the head and neck (SCCHN). In keeping with previous reports, expression of the deltaN- and p63alpha-isoforms predominated and deltaNp63 mRNA was expressed at significantly higher levels in tumours compared to matched normal tissues. Some tumours also expressed the highly efficient transactivator TA- and p63beta-isoforms, and p63beta was significantly increased in tumours compared to matched normal tissue. We could not identify any correlations between different p63-isoform expression patterns and proliferation, p53 status, or telomerase expression. All p63 isoforms could be identified in normal surface epithelium, and micro-dissection showed that the high levels present in basal layers were similar to those seen in tumour tissues. Thus, high-level expression of deltaNp63 in tumour cells may represent maintained expression by the basal cells from which the tumour arose, rather than representing a true over-expression of p63 during tumourigenesis. Tobacco usage, a genotoxic predisposing factor for SCCHN, had no effect on p63 expression in oral epithelium. Taken together, our data indicate that SCCHN maintain expression of high levels of deltaNp63alpha in combination with varying levels of other p63 isoforms, some of which are highly efficient transcriptional activators. The complexity of these p63 expression patterns seen in primary SCCHN indicates that p63 has multifaceted roles in tumour biology.