Stare into the eyes of a chimpanzee, meet the intelligent gaze that stares back at you and you will recognize a link with human beings that stretches back millions of years.

Now that link has become the centre of a heated and often emotional debate.

On the one hand are scientists who believe using chimps for medical research offers hope for many of the diseases that plague mankind.

On the other are opponents, some of them also scientists, who say this research is cruel, unnecessary and ultimately a waste of money.

Just inside the gates of the Fauna Foundation, a sanctuary for chimps near Montreal, is a large, metal cage. It's there to remind visitors of the price chimps have paid as unwilling subjects for medical research. Some of the 12 animals who live at Fauna were once housed in cages like this at a research facility in New York State, suspended from the ceiling of bare, barrack-like rooms, their world reduced to a few square metres. The only time they left their cages was to be infected with HIV in a long, and ultimately futile, search for a cure for AIDS in the 1990s. When that research was abandoned, nobody wanted to look after the infected chimps until the Fauna Foundation stepped in.

"Fauna was the first sanctuary in the world to rescue HIV-positive chimpanzees," said Gloria Grow, the founder of the Foundation. "And the three that are left here at Fauna look pretty good on the outside, but we know on the inside, they're totally destroyed."

They live out their days in an environment designed to be as close to their natural habitat as possible. They have indoor and outdoor areas, grass and trees to play in and a series of islands enclosed by a moat and an electric fence. For a chimpanzee, it's a comfortable world, but one that also offers them the affection and respect from human beings they often lacked in research facilities.

"It's taken them a long time to trust humans again," said Gloria Grow. "They're like prisoners. Some days are good and some days are bad. So we start over each day in some cases."

Chimps aren't used for AIDS research anymore, but they are used for other types of studies. Right now, the United States and Gabon are the only two countries in the world that allow medical research on chimpanzees.

In Canada, there's no outright ban, but no one is actually doing it.

Instead, Canadians commission studies at research facilities like the New Iberia Research Center in Louisiana, the largest facility of its type in the world. It's home to nearly 7,000 primates, 360 of them chimpanzees.

"For some, research chimpanzees are actually absolutely critical," said Thomas Rowell, the director of the centre. "Some of the products that we work with, for example antibodies, target very specific receptors that are present only on human cells and on chimpanzee cells."

The chimpanzees at New Iberia live in an outdoor, zoo-like setting, divided into groups according to age and sex. They only move indoors when needed for a research project.

Now there is a bill before Congress that aims to stop using chimps in the United States, a ban that was prompted in part by an undercover operation at New Iberia in 2008 by the Humane Society of the United States. Using hidden cameras to shoot over nine hours of video, the investigation found evidence of alleged abuse at the centre. One scene showed a chimp being sedated by a dart gun and allowed to fall to a concrete floor. Another showed an unco-operative subject being hit in the teeth. The images went viral on the Internet and created a public relations disaster.

"There were five minutes or less of video where you said to yourself, you know, I wish so and so hadn't said this," said Thomas Rowell. "Or I wish they'd have been more careful here."

Since then, New Iberia says conditions have improved and the centre is trying to present a more humane face to the public. When W5 visited, we were shown new techniques for sedating chimps where the animals are trained to present their arm to receive an injection instead of a dart gun.

But no matter how hard places like New Iberia try to restore their image, opponents of using chimps for research are not appeased.

"Chimps are a tiny, tiny little fraction of the research conducted on animals," said Wayne Pacelle, President of the Humane Society of the United States. "And the vast majority of scientists long ago decided: too expensive, too difficult to handle, too smart. We shouldn't be doing it."

If the research is banned, it will create a new problem. All those animals -- around a thousand in all, mostly at New Iberia -- still need to be fed and housed.

"They still have to be paid for," said Thomas Rowell, the Director at New Iberia. "Whether these animals are being maintained in sanctuaries or whether they're being maintained at the research centres, they still need to be supported."

One place they won't be going to is the Fauna Foundation in Quebec.

"Fauna is not taking any more chimpanzees," said the founder of the Fauna Foundation, Gloria Grow. "Smart, sensible sanctuaries with older directors without a succession plan really shouldn't be taking on any more than we have."

But, according to the Humane Society of the United States, the U.S. Congress already has legislation in place that could deal with this issue. "A thousand is actually a pretty manageable number," said Wayne Pacelle. "We rescue all kinds of animals, find places for them. Where there's a will, there's a way."