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We must begin this story by telling you what federal officials deny. They deny that they are in any way admitting that vaccines cause autism. The story, though, is about the reason they had to issue that denial. The government has agreed to award damages from a special vaccine compensation fund to the family of a girl with symptoms of autism.

Autism activists are already using that case to back up their claims about vaccine dangers. Caught in the crossfire is a program that is supposed to compensate families whose children suffer rare injuries that are definitively linked to vaccines.

NPR's Julie Rovner has more.

JULIE ROVNER: At a news conference on the steps of the federal courthouse in Atlanta yesterday, John Gilmore of the group Autism United pulled no punches.

Mr. JOHN GILMORE (Autism United): For the first time the court has conceded in a case that vaccines can indeed cause autism.

ROVNER: But federal officials say that's not they've done. As part of a ruling that's supposed to be confidential, lawyers for the Department of Health and Human Services agreed to pay an as-yet-undetermined amount from the Federal Vaccine Injury Compensation Program to the family of nine-year-old Hannah Poling.

Hannah was developing normally until she received a series of shots when she was a year-and-a-half old. After that she began to regress and developed autistic-like symptoms. Further testing determined Hannah had an underlying disorder in her cells, a so-called mitochondrial disease. That can cause symptoms similar to autism.

And in its ruling, the government said it was possible that the vaccines Hannah received may have exacerbated that disorder.

Charles Mohan, CEO of the United Mitochondrial Disease Foundation, says he finds the government's concession in this case reasonable.

Mr. CHARLES MOHAN (CEO, United Mitochondrial Disease Foundation): It could have been the vaccine that exacerbated that particular underlying mitochondrial disease. Or in a lot of cases it's the onset of a virus, an infection, a flu that could have the same impact.

ROVNER: But at the same time, says Mohan, there's no scientific evidence to suggest the vaccines themselves can cause either mitochondrial disorders or autism. That's something federal public health officials stressed yesterday. Julie Gerberding heads the Centers for Disease Control and Prevention.

Ms. JULIE GERBERDING (Centers for Disease Control and Prevention): The government has made absolutely no statement indicating that vaccines are a cause of autism. That is a complete mischaracterization of the findings of the case and a complete mischaracterization of any of the science that we have at our disposal today.

ROVNER: But that remains a hard sell to parents of autistic children, like Becky Estepp of Poway, California. She says the reaction her son Eric had to a hepatitis B vaccine in 1998 was immediate and severe. Not only did he begin to suffer a myriad of physical problems...

Ms. BECKY ESTEPP (Parent): At the same time his speech wasn't developing as much any longer and he kind withdrew from our world and turned into himself.

ROVNER: Symptoms like those led Estepp and other autism activists to search for a vaccine/autism link. Many think that link may be the preservative thimerosal, a mercury derivative no longer used in most vaccines.

Now Estepp represents one of nearly 5,000 families of children with autism who filed for damages from the federal Vaccine Injury Compensation Program. That's nearly twice as many families as the program has compensated since its inception two decades ago. And most of those awards were for well-documented side effects that occur in a small number of cases; things like getting polio from the oral polio vaccine.

Paying claims to all those children with autism would quickly bankrupt the program.

Representative HENRY WAXMAN (Democrat, California): There's no question this is the biggest challenge to the vaccine compensation system that it's ever seen.

ROVNER: That's California Democratic Congressman Henry Waxman. He wrote the law that created the vaccine compensation system in 1988. He says the program is threatened no matter what happens. If the families of autistic children win compensation, there won't be enough money to pay all their bills. But if compensation is denied those families, he says, they'll probably go to court instead.

Rep. WAXMAN: Which could scare off the manufacturers from deciding to even stay in this business.

Vaccine manufacturers won't say that outright, but they voice another worry, that if the vaccine program awards money to families for autism, other parents might be afraid to vaccinate their children.

Thomas Netzer is with drug and vaccine maker Merck

Mr. THOMAS NETZER (Merck): In fact, there'd be a real risk, I believe, that diseases which have been controlled in the United States and which used to cause very high morbidity and mortality - in fact thousands of deaths every year - could once again become common in the United States. That would not be a good outcome.

ROVNER: With the government's concession in the Georgia case, it won't have a formal hearing. But a total of nine other test cases are being heard by the vaccine injury compensation program - testing various theories of whether vaccines alone, thimerosal alone, or a combination of the two, could cause autism. It could be a year before all those cases are decided.

Julie Rovner, NPR News, Washington.

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