Bowenoid papulosis is considered by some authors to be a form of high-risk genital warts, but more recently is now thought to be an early form of cancer caused by a variety of high-risk human papilloma viruses (HPV), usually HPV 16 and 18. The lesions are described as flat, sometimes dark, bumps often found in clusters near or on the genitalia of both men and women. Women may not even know they have lesions as they commonly occur internally on the cervix.   
Bowenoid papulosis is concerning because they appear to look like genital warts, but under the microscope a biopsy of bowenoid papulosis shows early features of superficial squamous cell carcinoma. It is very important to have genital/rectal lesions evaluated by a physician. Women are at greater risk for cervical cancer if they or their partners have bowenoid papulosis.
Individual warts may be treated by a variety of methods but the virus itself is difficult to eradicate. If the biopsy shows cancerous changes then the lesions should be removed and treated similar to a skin cancer. Podophyllin is a topical therapy that can be applied to some warts depending on location.   Imiquimod (Aldara) may also be applied to most warts.

Cryotherapy may be utilized, which involves applying liquid nitrogen and destroying the wart by freezing the tissue. Various acids are also used to treat genital warts. For Bowenoid papulosis specifically, 5-FU 5% cream is utilized with good success. Any warty lesion in the genital area should be biopsied first to rule-out any cancerous changes.   New HPV vaccines have been approved and recommended by the CDC to help prevent cervical cancer in women.