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Recurrent laryngeal papillomatosis (RLP) is, although benign, a challenging disease for both, the patient and the treating physician. Maximum disease control with minimum intervention is considered to be the gold standard. However, patients have to undergo repeating surgical interventions. Human papillomavirus (HPV), mainly so called low risk types, are thought to be responsible for the development of RLP. But, there is still some controversy over the true prevalence of HPV and the virus-specific molecular diagnostic of choice. Therefore archival tissue samples from 44 patients with RLP at laryngeal site, out of which eight developed laryngeal cancer, was screened for presence of HPV through various molecular approaches. Results from these different methodologies were compared between each other and with patient's characteristics. The overall detection rates of HPV with the various methods used in this study were: HPV16 E6/E7 PCR: 0%; GP5+/6+ PCR: 4.5%; CDKN2A/p16 immunohistochemistry: 6.8%; in-situ hybridization for low and high risk HPV types: 52.3%; HPV6/11 L1 PCR: 72.7% and HPV6/11 E6 PCR: 79.5%. Disease progression showed no apparent dependence of the detected HPV type or clinical variables like age at diagnosis, sex, or additional drug application (Cidofovir and Bevacizumab). In conclusion, the broad-spectrum PCRs alone or in combination with immunohistochemistry of CDKN2A/p16 and in-situ hybridization are unsuitable for HPV detection in RLP. Based on the findings presented in this study the type specific PCRs targeting the E6 open reading frame are clearly superior in detection of HPV in this tumor entity. J. Med. Virol. 87:860–870, 2015. © 2015 Wiley Periodicals, Inc.