While expressing sympathy for the parents involved in the emotionally charged cases, the court concluded they had failed to show a connection between the mercury-containing preservative and autism.
"Such families must cope every day with tremendous challenges in caring for their autistic children, and all are deserving of sympathy and admiration," special master George Hastings Jr. wrote.
But, he added, Congress designed the victim compensation program only for families whose injuries or deaths can be shown to be linked to a vaccine and that has not been done in this case.
The ruling came in the so-called vaccine court, a special branch of the U.S. Court of Federal Claims established to handle claims of injury from vaccines. It can be appealed in federal court.
The parents presented expert witnesses who argued mercury can have a variety of effects on the brain, but the ruling said none of them offered opinions on the cause of autism in the three specific cases argued. They testified that mercury can affect a number of biological processes, including abnormal metabolism in children.
Special master Denise K. Vowell noted that in order to succeed in their action, the parents would have to show "the exquisitely small amounts of mercury" that reach the brain from vaccines can produce devastating effects that far larger amounts ... from other sources do not. The ruling said the parents were arguing that the effects from mercury in vaccines differ from mercury's known effects on the brain. Vowell concluded that the parents had failed to establish that their child's condition was caused or aggravated by mercury from vaccines.
Friday's decision that autism is not caused by thimerosal alone follows a parallel ruling in 2009 that autism is not caused by the combination of vaccines with thimerosal and other vaccines.
The cases had been divided into three theories about a vaccine-autism relationship for the court to consider. The 2009 ruling rejected a theory that thimerasol can cause autism when combined with the measles-mumps-rubella vaccine. After that, a theory that certain vaccines alone cause autism was dropped. Friday's decision covers the last of the three theories, that thimerosal-containing vaccines alone can cause autism.
The ruling doesn't necessarily mean an end to the dispute, however, with appeals to other courts available.
The new ruling was welcomed by Dr. Paul Offit of Children's Hospital of Philadelphia, who said the autism theory had "already had its day in science court and failed to hold up."
But the controversy has cast a pall over vaccines, causing some parents to avoid them, he noted, "it's very hard to unscare people after you have scared them."
On the other side of the issue, a group backing the parents' theory charged that the vaccine court was more interested in government policy than protecting children.
"The deck is stacked against families in vaccine court. Government attorneys defend a government program, using government-funded science, before government judges," Rebecca Estepp, of the Coalition for Vaccine Safety said in a statement.