In a world first, an anti-cancer vaccine usually given to high school girls will be extended to some Australian boys from next year.

Four out of five people are believed to have been exposed to human papilloma virus (HPV), which can cause genital warts and cervical cancer.

A vaccine developed in Queensland has been given to young girls since 2007. Ever since, there have calls to broaden the scheme to include boys.

Federal Health Minister Tanya Plibersek says boys aged 12 and 13 will now be given three doses of the Gardasil vaccine under the National Immunisation Program.

"This is a very important next step in the story of Gardasil," she said.

"It's a very exciting journey, an Australian invention, a world-first vaccine for women and now a world-first vaccine for young men."

Ms Plibersek says year 9 boys will also be able to get the vaccine at school under a catch-up program for the next two years.

Gardasil was first made available to teenage girls free of charge in 2007, and Ms Plibersek says it has already had an impact.

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"Significantly reducing the number of lesions that lead to cervical cancer among women in the vaccinated age group," she said.

"It is estimated that a quarter of new infections will be avoided by extending the vaccine to boys."

The vaccination program for boys is expected to cost $21.1 million over four years.

Ms Plibersek says the cost will include around 870,000 vaccinations, an information campaign, a vaccine register and monitoring of adverse reactions.

Campaigning for change

Many health experts have spent years campaigning for the change.

A breakthrough came last year when the Pharmaceutical Advisory Committee recommended the Immunise Australia Program be widened to include vaccinating boys in their first year of high school.

Steve Hambleton, the president of the Australian Medical Association, says today's announcement will make Australia a leader in the battle against the sexually transmitted virus.

He says HPV is known to cause a variety of cancer types in both men and women.

"Persistent HPV infections is associated with approximately 85 per cent of anal cancers, 50 per cent of penile cancers, 70 per cent of vaginal cancers and 40 per cent vulval cancers and so treating both men and women will decrease the prevalence of these diseases significantly," he said.

Professor Ian Frazer is the brains behind the Gardasil vaccine. In 2006, he was named Australian of the Year but he still endured plenty of criticism.

Judy Wilyman from Wollongong University argues the link between HPV and cervical cancer is based on assumptions.

In an article published by the British Society for Ecological Medicine, she says 90 per cent of women infected with the virus do not develop the disease.

But Dr Hambleton disagrees.

"This is one of the most potent vaccines that we have and we know that cervical cancer in women is related to HPV vaccine but with anal cancers, penile cancers, it is timely that it is actually extended to boys," he said.