Bowenoid papulosis (BP) is characterized clinically by its benign-looking appearance and histologically by the features of high grade squamous intraepithelial lesions (SILs). The external genitalia of young people is a common site of occurrence, and most of the lesions undergo resolution by local treatments or even spontaneously. A strong association between BP and high risk types of human papillomavirus (HPV), especially HPV 16, has been reported and the incorporation of BP into the SIL category is generally accepted, but controversy still exists as to the true nature of BP. We analyzed the clonality of BP lesions occurring on both sides of the vulva of a 15–year-old girl. DNA was subjected to a polymerase chain reaction-based clonal analysis using the highly informative androgen receptor gene (HUMARA) with a nonisotopic modification. The clonal analysis of each BP lesion showed a random X-chromosome inactivation pattern, indicating a polyclonal nature of this disorder. Although monoclonal proliferation of vulvar SIL was recently reported, this is the first report of the polyclonality in a type of SIL diagnosed as BP, supporting a clinicopathologic heterogeneity in SIL of the vulva.