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.
Several deaths associated with the vaccine led doctors to advise caution in the rush to promote widespread use of the vaccine, and doctors say there is a lack of public awareness of its role in preventing cancer.
"With any new vaccine, you have to err on the side of caution, but every year we know more about it," said Deeken. "But we have to ask the question: What do we do for the spouses and kids of our patients? I don't see any downside to vaccination at this time. My son and daughter will get it."
Because humans are the only reservoir for HPV, "it could be eliminated like smallpox," he said.
The research isn't new, but it has not received wide attention, perhaps because of taboos associated with oral sex.
Oral sex has become more commonplace; people have more sex partners and have sex earlier in life -- all behaviors linked to HPV-related oral cancers, according to a study in the Centers for Disease Control and Prevention's (CDC) Emerging Infectious Diseases report.
A study at the Swedish Karolinska Institutet showed the risk of developing oral HPV infection increased with a rise in lifetime oral or vaginal sex partners. It also cited "open mouth kissing."
The study included 542 American students, and noted similar increases in such cancers in Britain, Finland and The Netherlands.
But Dr. Kevin Cullen, director of University of Maryland's Marlene and Stewart Greenebaum Cancer Center, is not sure only oral sex is to blame.
"It's hard for me to believe sexual behaviors have changed that much in 15 to 20 years," he said. "It may be that as happens, epidemics get enough people infected and an infection begins to take off, and that may have happened with HPV at some point."
A study Cullen did last year found that HPV-related oral cancer in African Americans were less common than whites, perhaps because of negative cultural attitudes about oral sex.
"But it looks like blacks are beginning to catch up with whites," said Cullen.
Scientists also don't know why women tend to develop cervical cancer while men have more throat cancer. "Maybe women are better able to transmit to a man than a man to the oral mucosa of a woman," said Cullen.
Doctors also think that cancer is likely to develop in the first area of exposure ? in women, usually the vagina. The woman may then develop later immunity in the throat.
But with more oral sex, often before vaginal sex, female throat cancers could increase, they say.
Very little HPV was seen until the 1980s. "It was very rare in our archives," said Cullen. "But each year we looked, it was more prevalent. Why, no one is really sure."
And doctors say those numbers have not yet peaked.
"There is increasing evidence that boys as well as girls should be vaccinated," said Cullen. "Men and women are increasingly going to face the burden of cancer, and we have a tool to prevent it."
Why the medical community has not fully embraced vaccination is not clear.
"The lead time for development of oral cancer is in decades, so to do definitive studies would take decades to do," he said. "[The FDA] picked the simpler task of preventing HPV warts in the short time frame."
Resistance has also come from safety concerns, as well as the fear by some groups that vaccination for a sexually transmitted disease will promote sexual behavior.
Cervical cancer just may just be "sexier" than throat cancer, said Dr. Ranit Mishori, a family physician in the Georgetown University School of Medicine.
"We don't think about oral cancer except in smokers," she said. "There is no question HPV is the cause of most oral cancers, but it's partly an awareness issue relating to our kids' sex life, and who wants to talk about oral sex?"
Convincing parents to vaccinate their sons as well as their daughters is a "hard sell," said Mishori.
"Oftentimes it's the moms who take the kids to the doctor, and we tell them we have this great vaccine that can prevent their daughter from getting cervical cancer," she said. "Moms can easily relate."
But it's harder to tell her "to give her son three painful shots so that he won't transmit it to his girlfriend in the future and might not transmit cancer or have oral cancer himself," said Mishori.
As for potential side effects with the vaccine, Mishori said those concerns are "pretty minor compared to the potential."
"It hasn't been around too long, but it's been tested on thousands of women," she said. "The fact that the vaccine prevents cancer is astounding in itself."