Summary Background  Bowen's disease in the genital area is generally considered to be caused by mucosal high‐risk human papillomaviruses (HPVs). However, the detection rate and spectrum of HPVs in extragenital Bowen's disease are various and it is not clear to what extent HPV is involved in its pathogenesis. Objectives  To assess the degree of association of HPV in extragenital cases by examining detection rates, types, quantities and localization of HPV. Methods  A polymerase chain reaction (PCR) approach that we had previously established, which can give sensitive detection of a broad range of HPVs from cutaneous including epidermodysplasia verruciformis‐related HPVs (EV‐HPVs) to mucosal HPVs, was applied to samples from 41 patients with extragenital Bowen's disease and normal skin samples from 48 individuals. Semiquantitative L1‐PCR and tyramide‐based in situ hybridization (ISH) were also employed for positive cases. Results  HPVs belonging to the mucosal high‐risk group were detected in three patients with Bowen's disease (7%; two HPV 16 and one HPV 33), with 101−103 copy equivalents per diploid amount of cellular DNA. They were distributed among most nuclei of tumour cells but in none of the cells of adjacent normal skin. HPVs belonging to the cutaneous group were detected in two patients (5%; HPV 27 and HPV 76) at 10−2−10−3 copy equivalents, the same level as in a normal skin specimen positive for type 23 EV‐HPV. No positive signals were observed by ISH. Conclusions  HPVs belonging to the mucosal high‐risk group may participate in the development of extragenital Bowen's disease.