Parents of boys face some uncomfortable realities when choosing whether to have their child vaccinated. The burden of disease in males results mostly from oral or anal sex, but vaccinating boys will also benefit female partners since cervical cancer in women results mostly from vaginal sex with infected males.

Vaccinating the nation’s 11- and 12-year-old boys will cost almost $140 million annually, but the one-time catch-up among males 13 to 21 will cost hundreds of millions more. The government generally pays for about half of all vaccinations.

The committee has become increasingly concerned about the cost effectiveness of vaccines, since the newest vaccines tend to be very expensive while protecting against diseases that affect fewer people. Vaccinating boys is cost effective when vaccination rates in girls are relatively low, which they are now. Fewer than half of girls between the ages of 13 and 17 have received at least one dose of the HPV vaccine, and fewer than a third have received all three doses.

Only about 1 percent of boys have received the HPV vaccine, even though the vaccine advisory committee has said that boys could be vaccinated against the disease if they or their parents wished.

Vaccinating homosexual boys would be far more cost effective than vaccinating all boys, since the burden of disease is far higher in homosexuals. “But it’s not necessarily effective or perhaps even appropriate to be making those determinations at the 11- to 12-year-old age,” said Kristen R. Ehresmann of the Minnesota Department of Health and a committee member.

Dr. S. Michael Marcy, a clinical professor of pediatrics at the University of Southern California and a committee member, said that the money needed to vaccinate 11- and 12-year-old boys would pay for only a few hours of the war in Afghanistan while potentially saving thousands of lives in the United States.

“I’m constantly being told we don’t have the money. Well, we do have the money,” Dr. Marcy said. “We need a new set of priorities, and we if we don’t set those priorities, who will?”