He said the boys had conditions that made them especially vulnerable to the mercury in thimerosal.
"The evidence is indirect and it is circumstantial but it is supportive of the general theory of causation," he said.
No one knows what causes autism, which can severely disable a child with symptoms ranging from severe social avoidance to repetitive behaviors and sometimes profound mental retardation.
The U.S. Centers for Disease Control and Prevention estimates that about one in every 150 children has autism or a related disorder such as Asperger's syndrome.
Doctors agree there is a genetic link, and probably that something in the environment, possibly even conditions in the womb, can cause the brain effects that lead to symptoms.
While many studies have shown the thimerosal in vaccines has not caused autism, a vocal group argues the government and other experts are ignoring or covering up the evidence. Thimerosal has now been removed from most childhood vaccines.
"I think we will be able to convince you that the epidemic is real, that the increase is real," Mike Williams, another attorney for the boys, told the three "special masters" hearing the cases.
"The debate is over. There is no controversy," government attorney Lynn Ricciardella retorted in her opening arguments.
"The credible scientific community has already spoken on this issue and has rejected it."
Some autism activists have seized on the case of Hannah Poling, a girl from Georgia who won a case claiming a vaccine caused autism-like complications from a rare disorder.
The activists say it proves the federal courts gave in on the argument, but the government says Poling's case, which was removed from the special process and heard separately, was an exception and cannot be used as a precedent.
