The vaccine targets four specific subtypes of the virus -- types 6, 11, 16 and 18.
HPV types 16 and 18 cause 70 percent of cervical cancer cases. Types 6 and 11, on the other hand, while much more common are responsible only for genital warts.
The infection rate of the four HPV types contained in the HPV vaccine was 3.4 percent, which suggests that 3.1 million women in the United States may be infected with these strains.
Much of the debate surrounding the HPV vaccine concerns the young age at which females are recommended to receive the shots.
The Centers for Disease Control and Prevention (CDC) currently recommends that all girls ages 11 to 12 be vaccinated. This is because the vaccine works best if the recipient has not yet been exposed to the virus.
According to a CDC spokesperson, the results of the study will not change their vaccination recommendation.
However, some opponents of mandatory vaccination programs for preteen girls argue that vaccinating these girls may encourage them to be sexually active at a younger age.
But previous studies have shown that some girls even younger than 14 are infected with HPV. Dr. Diane Harper, a gynecologist at Dartmouth Medical School, reports, "There is no one age at which all females are not infected with HPV."
And in the current study, at least one of the four HPV types in the vaccine was detected in 6.2 percent of females ages 14 to 19 years.
Harper says vaccination against HPV does not provide 100 percent protection against cervical cancer, and women still need to have regular Pap smears as recommended by their doctor to allow for early detection of changes in the cervix.
"Vaccination is not a substitute or a replacement for Pap testing," she says. "Vaccination without Pap testing will lead to an increase in cervical cancers in the U.S."
Dr. Steven Goldstein, professor of obstetrics and gynecology at the New York University School of Medicine, agrees. "The Pap smear is the greatest triumph epidemiologically in modern medicine, and this whole HPV vaccine threatens to undermine that."