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HPV infection in the superficial cells of the oral mucosa could reflect the presence of HPV in head and neck cancer cells. Due mostly to the use of heterogeneous analytical methods, discordant data exist in the literature regarding the agreement between the presence of HPV in non-neoplastic oral mucosa and in tumour tissue from the same patient. The presence of HPV DNA and viral types were compared in paired cytological and biopsy samples from 56 patients with head and neck neoplastic and preneoplastic lesions using the highly sensitive SPF10 LiPA Extra assay, which has been validated recently for formalin-fixed paraffin-embedded tissue using paired cervical cytology and biopsy samples. Kappa statistics were used to measure the inter-rater agreement. The overall agreement with respect to HPV infection was 96.43% (kappa=0.8367). For 76.79% of subjects (kappa=0.6937), the same number of HPV types was detected in cytological and biopsy specimens. The overall positive typing agreement was 90.90%, comprising 130 out of 143 individual HPV type analyses. The agreement shown was good for HPV 18, 44, 45, 54 and 66 (kappa=0.6585-0. 7321), excellent for HPV 6, 16, 40, and 54 (kappa=0.8108-0.8679), and absolute for HPV 11, 31, 33, 35, 39, 51, 52, 53, 59, 74, and 69-71 (kappa=1.0000). The high sensitivity of the SPF10 LiPA and its excellent performance both for recognising HPV infection and for identifying the viral types present in tumour tissue and in oral exfoliated cells make it a useful method for the assessment of HPV infection in patients with head and neck cancer. The excellent agreement for HPV infection and genotyping in paired samples suggests that oral exfoliated cells can be used for HPV detection in the head and neck region., (Copyright © 2012 Elsevier B.V. All rights reserved.)