In men, genital warts appear on the penis, scrotum, or anus, while in women they tend to occur on the vulva, but may also occur on the cervix, vagina, anus, or the perineum between the vulva and anus. Genital warts can also develop in the mouth and throat of someone who has had oral contact with the genitals of an infected person.

The warts appear like small, flesh-colored bumps, flat lesions, stem-like protrusions, or cauliflower-like growths. Genital warts can be as small as one millimeter in diameter or may appear in clusters that cover large areas. Genital warts usually do not cause pain or discomfort.

In females, some types of HPV can cause changes in the cells of the cervix which are associated with an increased risk of cervical cancer. These types are called high-risk HPV. The types of HPV that cause genital warts are low-risk HPV and tend not to be associated with cancer. However, since anyone can be infected with multiple types of genital warts, the presence of genital warts does not rule out the possibility of a co-infection with a high-risk type of genital warts that is associated with increased cancer risk.