Aims: Currently there are no diagnostic techniques that can precisely determine the primary site of a metastatic squamous cell carcinoma (SCC). Anogenital SCC has a high prevalence of high-risk (HR) human papillomavirus (HPV) DNA, particularly in the cervix where the value approaches 100%, whereas non-anogenital SCC generally has a low prevalence. The aim of this study was to examine whether the finding of HR HPV DNA in a fine needle aspiration (FNA) of metastatic SCC could be used to determine a likely anogenital origin.Methods: Polymerase chain reaction (PCR) and viral sequencing were used to identify HR HPV DNA in cell block and needle rinse material derived from FNA samples in a series of metastatic SCC.Results: HPV DNA was detected in nine of 12 (75%) metastatic anogenital SCC, and type 16 was sequenced in seven. HPV DNA was detected in only one of 18 (5.6%) metastatic SCC from other sites such as lung, oral cavity and skin. The positive control case was an oral cavity tumour and type 33 was sequenced.Conclusions: Although reservations remain, particularly in relation to the prevalence of HPV DNA in non-anogenital sites, HPV DNA testing by PCR: (1) can be successfully performed on FNA material, and (2) in the correct clinical context, can guide clinicians in assigning a site of origin. HPV DNA detection was the major indicator to the primary site in one occult tumour and several where the previous diagnosis of anogenital cancer was not known at presentation.