Human papillomaviruses (HPVs) were detected in 69 (43.7%) of 158 and in 7 (4.5%) of 155 anogenital hairs obtained from 53 patients with genital warts (GWs) and from 53 age-matched healthy control subjects, respectively. At least 1 hair sample was positive for 69.8% of patients and for 13.2% of control subjects. For patients, HPV was detected in 64.2%, 39.6%, and 26.9% of hairs plucked from the pubic, scrotal, and perianal regions, respectively. For 91.9% of patients, the same HPV genotype was identified in GWs and hairs from at least 1 sampling site. Having GWs was found to be strongly associated with the presence in anogenital hairs of the HPV genotype causing the GWs (range of odds ratios, 13.0-20.0).