The decision follows a recommendation from an FDA's advisory committee, which voted last month that the vaccine -- already approved for preventing cervical and vaginal cancer in women and genital warts in both sexes -- is safe and effective for anal cancer prevention.
A randomized trial that included men who have sex with men, ages 16 to 26, was the main basis for the new approval. It found that Gardasil was 78 percent effective in preventing anal cancer related to the virus.
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Because the disease process of anal cancer is believed to be the same in females as in males, and because the cancer usually develops during adulthood, the FDA did not require separate studies in females or in preteens.
The FDA emphasized that HPV vaccination would not prevent anal cancer in individuals already infected with the virus.
"Treatment for anal cancer is challenging; the use of Gardasil as a method of prevention is important as it may result in fewer diagnoses and the subsequent surgery, radiation, or chemotherapy that individuals need to endure," said Dr. Karen Midthun, director of the FDA's Center for Biologics Evaluation and Research, in a statement.
Although anal cancer is uncommon in the general population, the incidence is increasing, the agency indicated.
About 90 percent of anal cancers are believed to stem from HPV infection. The American Cancer Society estimates that about 5,300 people are diagnosed with anal cancer each year in the U.S., affecting more women than men.