To investigate the prevalence and the natural history of human papillomavirus infections, we monitored HPV DNA shedding as a consequence of immunosuppression, with the expectation that latent viral infections would reactivate and become detectable. The study populations consisted of women who were in end-stage renal failure, those who ultimately received kidney transplantations, and those who had HIV/AIDS with various degrees of immune depression at entry. For each woman, cervico-vaginal lavage to sample viral shedding from the lower genital tract was performed at approximately six month intervals, and the cohorts have been followed since 1996. Nested polymerase chain reaction amplification of papillomavirus DNA using novel pairs of primers was followed by diagnostic restriction endonuclease cleavage or by DNA sequencing. This strategy is particularly capable of identifying single and multiple infections and determining the genotypes of any viruses present. Of the 225 women in the HIV cohort, 177 (79%) were HPV-positive and 111 (49%) shed from two up to eight different HPV types over the course of the survey. Thirty-five different mucosotropic HPV types, virtually all that have ever been described worldwide, were isolated from these 225 women, and nine additional new (provisional) types were discovered. As is always the case, HPV-6 was very common. However, all the other frequently detected HPV types (45, 52, 53, 54, 58, 74) were more prevalent than the types typically reported forthe general population (HPV-11, 16, 18, 31, 33, 35). Notably, the 14 members of the A3 phylogenetic subgroup (HPV-61, 62, 72, 81, 83, 84, and all the new types) were by far the most frequently observed viral types in the AIDS cohort. The HPV prevalence in the cohorts of kidney transplantation candidates and recipients was only slightly lower than that in the AIDS cohort. We conclude that HPV infections are extraordinarily common and are normally held in a sub-clinical state by functional immune systems, but can be reactivated by immunosuppressive conditions. The question of how so many distinct types persist in the human population and can be repeatedly isolated from specimens collected around the world raises complex issues concerning the nature of viral transmission, reproduction, shedding, and mutational drift. These molecular epidemiological observations signal the likelihood that HPV is part of the commensal microflora of human epithelia. Their prevalence elicits a caution that latent HPV DNA may be present in primary human epithelial tissues.