Several studies have found human papillomavirus virus (HPV) in tissue from head and neck squamous cell carcinomas (HNSCCs), although the number of positive cases varies greatly from study to study. The extent and molecular epidemiology of HPV in HNSCC were assessed within cases drawn from southeast Scotland by performing broad-spectrum, real-time HPV polymerase chain reaction (PCR) on DNA extracted from 100 cases of HNSCC in formalin-fixed, paraffin wax-embedded material. All HPV-positive specimens were genotyped and sampled by laser capture microdissection. Pure samples of tumour, and, where possible, dysplastic and normal epithelium were then submitted for further HPV PCR and genotyping to investigate the sensitivity of the technique in small tissue samples. 10 of 100 cases tested positive for HPV, with 8 of these being derived from Waldeyer's ring. HPV DNA was found in adjacent epithelium in two of four cases where this was available. These findings confirm that HPV is likely to be involved in a subset of HNSCC in this population and that successful amplification of HPV nucleic acid is possible even using small amounts of paraffin wax-embedded tissue.