A large number of human papillomavirus (HPV) types, distributed over five papillomavirus genera, are detectable in the skin. HPV types belonging to the alpha, gamma, and mu genera have been detected in cutaneous warts. A state-of-the-art HPV genotyping assay for these cutaneous wart-associated HPV types does not exist although warts constitute a highly prevalent skin condition, especially in children (33%) and organ transplant recipients (45%). Cutaneous warts are again the focus of attention as their clinical relevance rises with the increasing number of chronically immunosuppressed patients. The objective of this study was to develop and evaluate a DNA-based genotyping system for all known cutaneous wart-related HPV types using PCR and Luminex xMAP technology. The broad-spectrum PCR amplified DNA of all known wart-associated HPV types from the genera alpha (HPVs 2, 3, 7, 10, 27, 28, 29, 40, 43, 57, 77, 91, and 94), gamma (HPVs 4, 65, 95, 48, 50, 60, and 88), mu (HPVs 1 and 63), and nu (HPV41). The probes were evaluated using plasmid HPV DNA and a panel of 45 previously characterized cutaneous wart biopsy specimens showing high specificity. HPV was also identified in 96% of 100 swabs from nongenital cutaneous warts. HPV types 1, 2, 27, and 57 were the most prevalent HPV types detected in 89% of the swabs. In conclusion, this Luminex-based genotyping system identifies all known cutaneous wart HPV types including phylogenetically related types, is highly HPV type specific, and is suitable for large-scale epidemiological studies.Papillomaviruses (PV) constitute a group of viruses associated with benign and malignant proliferative lesions of cutaneous and mucosal epithelia. The taxonomic family of PV includes 16 genera (5). More than 100 human papillomavirus (HPV) types have been fully sequenced. The number of HPV types that are not yet fully characterized is probably much larger. HPV types, distributed over five genera (alpha, beta, gamma, mu, and nu) and 16 species, infect the skin (5). HPV types belonging to species of three genera (alpha, gamma, and mu) have most frequently been detected in hyperkeratotic skin lesions (warts).The alphapapillomavirus (alpha-PV) types infecting the genital mucosa (e.g., HPV16, HPV18, HPV6, and HPV11) are the best understood. HPV16 and HPV18 are the most prevalent types involved in the pathogenesis of anogenital (e.g., cervical) cancer, and HPV types 6 and 11 cause genital warts and laryngeal papillomas. The alpha-PV types belonging to species 2, 4, and 8, which have been detected in cutaneous warts, have been studied less thoroughly. At present the most frequently detected alpha-PV types in cutaneous warts are HPV types 2, 3, 10, 27, and 57 (3, 10, 12-16, 18, 19). Gamma-PV types, including HPV4, HPV60, and HPV65, have also regularly been detected in cutaneous warts (4,10,12,15). Mu-PV types, HPV1 and HPV63, have also been detected in cutaneous warts (7). HPV types included in the beta and nu genera have rarely been detected in cutaneous warts. Only Harwood and coworkers (13) hav...