There are two HPV vaccines currently available, both of which protect against the two principal cancer-causing types of HPV, HPV 16 and HPV 18. By CDC estimates, the two strains cause 15,000 malignancies in women and 7,000 in men every year. The two strains account for an estimated 70 percent of cervical cancers, about 70 percent of vaginal cancers and most vulvar cancers. HPV 16 by itself causes 85 percent of anal cancers.
In addition to protecting against HPV 16 and HPV 18, Merck's Gardasil protects against two other disease-causing strains, HPV 6 and HPV 11, responsible for 90 percent of genital warts as well as cervical cell changes. GlaxoSmithKline's Cervarix protects against HPV 16 and HPV 18, but also has been found to confer some protection against three other cancer-causing strains, HPV 31, HPV 33 and HPV 45.
Dr. Diane Harper, director of the Gynecologic Cancer Prevention Research Group at the University of Missouri-Kansas City called it "misguided to think that all boys will gain any health benefit from HPV vaccination."
She also noted that the effectiveness of the vaccine wanes in men "two to three years earlier than in women," and that the possibility of preventing other HPV-associated cancers "could only occur" if the vaccine's effects lasted for a lifetime.
She contended that "mass vaccination" to prevent the other HPV-associated cancers "puts large numbers of people at risk for harms from vaccination compared to both the personal and public health risk of anal, penile, and oropharyngeal cancers."
In a background memo leading up to the vote, the CDC estimated that routinely vaccinating 11- and 12-year-old boys would likely be cost-effective. If 1 million 12-year-old boys were vaccinated, over the course of a lifetime, they would prevent 2,381 cases of mouth and throat cancer; 633 cases of anal cancer and 169 cases of penile cancer, assuming the vaccine was 75 percent effective against those conditions.
ABC News' Brian Hartman contributed to this story.