There is an interesting article in today’s Slate Magazine covering the thimerosal issue and Robert F. Kennedy Jr’s involvement. It points out some of the flaws in the Geiers’ work:
The main Geier approach is to mine data from a CDC reporting system that contains a mishmash of real and garbage vaccine-injury allegations, according to the vast majority of the scientists who work in this area. The Geiers have found a sixfold increase in autism in children who got thimerosal-containing vaccines. But nearly all the reports of autism they tallied came after allegations of the vaccine link had been publicized in the newspapers. In other words, the Geiers report the public's response to a scare as if it were meaningful data.
And it talks about other possible reasons for the supposed increases in autism:
A far more obvious explanation for the increase in autism rates in California was the one that mainstream autism experts expounded: diagnostic changes, new laws that expanded federal payments to care for autistics, and greater parental awareness of these resources. In 1990, Congress made autism one of the disabilities that qualified for federal funding. Thereafter, states were obliged to report all cases of autism. In a Minnesota study, to take one example, admissions of autistic children to developmental programs jumped starting in the 1991 school year and continued to do so for a decade. Often these increases occurred within the same grade. For example, 13 autism cases were reported per 10,000 Minnesota 6-year-olds in the 1995-96 school year—that is, among children born roughly in 1989. Five years later, the prevalence rate for this cohort was reported at 33 per 10,000. These were the same kids. Between the ages of 6 and 11, they'd suddenly "become" nearly three times as autistic—or rather, doctors, parents, and school counselors were enrolling them in programs more aggressively.
The author concludes he doubts vaccines are the cause of autism.