The throat tumors it causes, called oropharyngeal cancers, occur in specific areas: the base of the tongue and the area just behind the mouth, including the soft palate, tonsils, and the side and back walls of the throat. Some oropharyngeal cancers are not caused by the virus, but by tobacco and alcohol; their rates have been decreasing as smoking has declined.

Throat cancers caused by HPV are more treatable than those not caused by the virus. Median survival in throat cancer patients with the virus is 131 months; without it, 20 months. Virus-related throat cancers are far more common in men than in women, a difference that has not been explained.

HPV is commonly found in the genital region and is transmitted by intimate contact. Usually the immune system fights off the infection, but in some people the virus persists and causes cancer.

There is no screening test for oropharyngeal cancers, no equivalent of the Pap test used to find precancerous growths on the cervix, Dr. Gillison said. Oropharyngeal cancers generally are not found until symptoms start: lumpy, swollen lymph nodes in the neck, or a lingering sore throat or earache.

Patients may need surgery, radiation or chemotherapy, or some combination of those treatments.

“The side effects can be horrendous,” Dr. Gillison said. “It’s a very difficult therapy to get through.”

Two vaccines, Gardasil and Cervarix, protect against HPV Type 16 and other strains of the virus that cause cancers and genital warts. But medical groups now recommend them only for girls, to protect against cervical cancer.

Researchers think the vaccines might also prevent some throat cancers, but cannot be sure unless the vaccines are specifically tested for that purpose. The manufacturers — Merck and GlaxoSmithKline — say they have no plans to study throat cancers. But Dr. Cullen said that the vaccines were likely to prevent the throat cancers, and should be given to boys too. He said he had no connection to vaccine companies.

Dr. Gillison said the vaccine companies had paid for her research in the past, but had no role in this study, which was paid for by the National Cancer Institute, Ohio State University and the Oral Cancer Foundation.