Some researchers say it's a matter of genetics, while others point to mercury toxicity, especially in vaccines. Central to many parents' search for a reason for their child's autism is the element mercury. Some doctors say mercury -- as a part of the preservative compound thimerosal collects in autistic children's bodies.

"We wrote a paper stating that autistics represented children in their infancy could not excrete mercury as well as controlled children and since those people at MIT and Arizona State have reproduced that. So it is not a joke," said Dr. Haley.

But the CDC doesn't buy Haley's argument. The latest CDC-supported study, in the New England Journal of Medicine just this fall, says researchers found no link between thimerosal exposures in children related and neuropsychological deficits in children. The study looked at 42 standard measures of childhood development, but did not test outcomes specifically used to assess autism.

"Your pruning your data. It's cherry picking what you want," said Dr. Haley. 

That troubled some looking for a thimerosal link -- but not as much as the background of those who conducted the study. Six of the 18 researchers conducting the study earned consulting fees from Merck, Wyeth, and a other pharmaceutical companies that make and sell vaccines that contain thimerosal.

"Where the financial part is involved is that if it is true, and if it can be proven that thimerosal has been causing all of these problems. Then they are liable for all of these hundreds and thousands of injured children who have been injured by the toxicity of thimerosal no one should ever underestimate the power of industry," said Dr. Engley.

"Our government agencies and I mean this with all sincerity. It hurts me to say this, but I think our government, the CDC and the FDA are just sold out to pharmaceutical companies. They are not going to do anything that is going to effect a commercial product that is worth a lot of money. And this is worth a lot of money. In two ways, one they sell a lot and two the lawsuits that would come out would be astronomical," said Dr. Haley.

"The CDC was in on the production and development of some of these vaccines the CDC cannot afford to admit thimerosal is toxic because they have been promoting it for many years," said Dr. Engley.

"We are in an impossible situation and I think once things get worse and there are more crisis with vaccines and more reverse reactions and rising rates of autism before congress will step in and do something and take a hard look," said Dr. Ayoub. I think we need reform from the top down. We have to serpate the drug company influence from these federal agencies. We have to strip down the CDC and rebuild it."

When asked, "Does this pose a conflict of interest to have drug companies doing these studies or sponsoring these studies?" Dr. Miles said, "Sure. I think you have to be very careful in any kind of research."

"Let's change it. I just want to change it. But you need to change it where it wouldn't happen again. You need to get the control of vaccines out of the hands of people who can make money with the government cause they will approve anything," said Dr. Haley.

We'll tell you what the centers for disease control had to say about our story in part 3 of our series which airs next Monday at 10 p.m.