Human papillomavirus (HPV) infection is emerging as a major prognostic and predictive marker in head and neck squamous cell carcinoma (HNSCC). Researches are focused on the development of HPV detection assays specially designed for HNSCC. The HPV diagnosis in these tumours is relevant toprognosis even in an already-developed tumour, whereas in the cervix, where the HPV is the cause of almost all tumours, this information has less clinical relevance. The better outcome of HPV-associated HNSCC raises the question about the best methodologies to distinguish between HPV and non-HPV-associated SCC. However, no consensus has been reached on the optimal way to identify HPV-associated SCC and ancillary studies have utilised many different methodologies, including HPV polymerase chain reaction testing, HPV in situ hybridization analysis, immunohistochemical staining for p16, and newer techniques that are currently under investigation. The objective of this review is to explain and give examples of various techniques of HPV detection highlighting how they might be used clinically. Although currently insufficiently specific due to the possibility of HPV infection originating at other sites, methodologies utilising serum and plasma to measure HPV infection will also be described, mostly for their potential future development and use. Finally, DNA/RNA microarray platforms will be briefly summarized for their capacity to identify the profile of molecular changes in any particular HPV+/HPV- cancer. In this way, it is expected to be possible to correlate the appropriate transcriptome-based diagnosis to the patients' specific cancer risk.