The vaccine has been recommended for girls since 2006 to prevent cervical cancer.
Experts say since then other cancers thought to be caused by HPV have increased, including anal and some head and neck cancers.
The AAP says the current approach isn't effective from a public health perspective since males are also participants in the spread of HPV.
The new guidelines are published on line in the journal Pediatrics.
They are in line with a recommendation made by the Centers for Disease Control.