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Generally the fact that a vaccine appears to be as safe as the manufacturer had promised shouldn't be news. It should be a given. But when it comes to the controversial vaccine against human papillomavirus (HPV), even the most straightforward data come with an asterisk.

The vaccine, called Gardasil and manufactured by Merck, is one of the first immunizations to protect against a cancer — in this case, cervical cancer, which is most commonly caused by infection with HPV. Because the virus is sexually transmitted, the Centers for Disease Control and Prevention (CDC) recommended in 2006 that girls get the vaccine at ages 11 and 12, before they become sexually active, so they have the best chance of avoiding the cancer and genital warts caused by HPV. States joined in, attempting to mandate HPV vaccination for school entry, but parents balked, in part because of concerns about encouraging promiscuity. It didn't help that girls were prone to fainting after getting the shot or that more than two dozen girls died shortly after getting immunized.

To address those concerns, researchers at the CDC and the FDA, which keep track of adverse events related to vaccines once they are approved, now report in the Journal of the American Medical Association (JAMA) that the rate of adverse events associated with the 23 million doses of Gardasil administered since 2006 is similar to the prelicensing rate among the 21,000 girls and young women who tested it in clinical trials and to that of other vaccines.

That should be reassuring. But the study did find that users of Gardasil faint and develop blood clots more often than those receiving other shots. The clots are extremely rare, though. In about 90% of these cases, the girls may have been more vulnerable to developing clots because they smoked or were overweight or on birth control pills. "Was it that this age group also tends to have these risk factors or did the vaccine have some sort of role?" asks the CDC's Dr. Barbara Slade, lead author of the paper. "We really don't know."

It's that uncertainty that is beginning to bother many physicians about the HPV vaccine. According to Dr. Charlotte Haug, editor in chief of the Journal of the Norwegian Medical Association and author of an editorial that JAMA published alongside Slade's paper, cervical cancer can be effectively picked up with Pap smears, a routine part of regular gynecological exams, and it's not clear that adding Gardasil to those screenings would significantly reduce a woman's chance of developing the disease.

Meanwhile, public health experts at Columbia University have a new study that shines a light on the marketing of Gardasil. They say Merck may be indirectly influencing doctors to use the vaccine by providing grants to professional medical organizations which then train and pay physicians to speak about the benefits of HPV vaccination. Merck denies the allegations. "The material developed by these societies is done independent of Merck and without any influence or review from Merck," says Dr. Richard Haupt, who heads the company's HPV-vaccine program.

As GlaxoSmithKline prepares to launch its own HPV vaccine in the U.S. and states continue to debate mandated immunizations, some doctors are taking a wait-and-see approach. "It's too early to begin to make decisions about mandates," says Dr. Joseph Bocchini, who chairs the American Academy of Pediatrics committee on infectious diseases. "We need more time to educate families and physicians and to get more data on the duration of immunity and safety." That's something many parents will agree with.

• Alice Park
• The Gardasil vaccine appears to be safe, but doctors are not ready to mandate immunization