But now, growing research in Europe and the United States is implicating HPV in a rising number of cases of head and neck cancers in men, and many doctors are recommending that all boys be vaccinated as well.
Doctors say that changing sexual behaviors -- earlier sex, more partners and especially oral sex -- are contributing to a new epidemic of orpharyngeal squamous cell cancers, those of the throat, tonsils and base of the tongue.
These cancers can be deadly, and are striking men at a younger age and in increasing numbers.
"There's a lag in information," said Dr. John Deeken, a medical oncologist at Georgetown University. "We physicians have done a poor job of advertising the fact that boys and girls should have the vaccine."
"This kind of cancer traditionally affects males who have been smoking and drinking all their life, and now in their mid-60s they are getting head and neck cancer," he said. "However, HPV cancer we are seeing in younger patients who have never smoked."
Two decades ago, about 20 percent of all oral cancers were HPV-related, but today that number is more than 50 percent, according to studies published by the American Association for Cancer Research.
Similarly high rates have also been seen in Europe, where a new Swedish study has shown a strong correlation between oral cancers and oral sex. Oddly, the rising rates have not been seen yet in the Southern Hemisphere in Australia and New Zealand.
Each year, more than 30,000 new cases of cancer of the oral cavity and pharynx are diagnosed, and more than 8,000 people die from oral cancer, according to the Centers for Disease Control and Prevention (CDC).
Cure rates are higher than for smoking-related throat cancers, but still only 50 percent.
Today, men are more likely to get oral cancer than are women, but as the epidemic grows, that could soon change.
"We expect in head and neck cancers that 85 percent are men and 15 percent are women," said Deeken. "But over the coming years that could become equal."
"It's going to take a couple of decades to see the trend turning around," he said. "The epidemiological risk factors are past sexual partners as well as marijuana exposure, not just oral sex."
HPV is the most common sexually-transmitted infection. Those who are infected often have no symptoms and pass it on to their partners through genital contact during vaginal and anal sex. It can also be transmitted during oral sex and, more rarely, during deep kissing through saliva.
There are more than 100 strains of the virus. Some cause genital warts, but others can result in cell changes that decades later can become cancerous. Each strain is identified by a number; oral and cervical cancers are caused by HPV sub-types 16 and 18.
HPV can also cause cancers of the vulva, vagina, penis and anus, and there is some evidence it is associated with esophageal and lung cancers.
The Food and Drug Administration (FDA) approved the use of Gardasil for girls in 2006 and for boys for treatment of genital and anal warts in 2009. The vaccine can be given at any age, though it is most effective given young people before any sexual exposure.
Doctors say it could prevent 10,000 more cases of oral cancer a year.