The special masters who decided the case expressed sympathy for the families, some of whom have made emotional pleas describing their children's conditions, but the rulings were blunt: There's little if any evidence to support claims of a vaccine-autism link.
The evidence "is weak, contradictory and unpersuasive," concluded Special Master Denise Vowell. "Sadly, the petitioners in this litigation have been the victims of bad science conducted to support litigation rather than to advance medical and scientific understanding" of autism.
Science years ago reached the conclusion that there's no connection, but Thursday's rulings in a trio of cases still have far-reaching implications - offering reassurance to parents scared about vaccinating their babies because of a small but vocal anti-vaccine movement. Some vaccine-preventable diseases, including measles, are on the rise, and last fall a Minnesota baby who hadn't been vaccinated against meningitis died of that disease.
The special court represented a chance for vindication for families who blame vaccines for their children's autism. Known as "the people's court," the U.S. Court of Claims is different from many other courts: The families involved didn't have to prove the inoculations definitely caused the complex neurological disorder, just that they probably did.
More than 5,500 claims have been filed by families seeking compensation through the government's Vaccine Injury Compensation Program, and Thursday's rulings dealt with the first three test cases to settle which if any claims had merit. The first cases argued that a combination of the measles-mumps-rubella vaccine plus other shots triggered autism.
"I must decide this case not on sentiment but by analyzing the evidence," said Special Master George Hastings Jr., writing specifically about Michelle Cedillo of Yuma, Ariz., who is disabled with autism, inflammatory bowel disease and other disorders that her parents blame on a measles vaccine given at 15 months.
"Unfortunately, the Cedillos have been misled by physicians who are guilty, in my view, of gross medical misjudgment," Hastings concluded.
CBS News medical correspondent Dr. Jon LaPook says there is a downside to continuing to look to make absolutely sure there's no link between vaccines and autism.
"A lot of experts are saying we're spending all this time and money looking at that potential link. We need to be spending it on early diagnosis and treatment," LaPook said.
Attorneys for the families said they were disappointed and may appeal.
"There was certainly no scientific proof that vaccines caused autism, but that's not the standard; the standard is likelihood," said Kevin Conway of Boston who represented the Cedillos. "We thought our evidence was solid."
"Certainly those three families are discouraged with the ruling," added Tom Powers, a Portland, Ore., attorney overseeing all the claims. "It's a big step, it's a significant step but it's not the last step."
Indeed, the court's ruling will do little to change the minds of parents who believe vaccines have harmed their children, said the head of a consumer group that questions vaccine safety, the National Vaccine Information Center.
"I think it is a mistake to conclude that because these few test cases were denied compensation, that it's been decided vaccines don't play any role in regressive autism," said Barbara Loe Fisher, the center's president.
The court still must rule on additional cases that argue a different link - that vaccines that once carried the mercury-containing preservative thimerosal are to blame, if the mercury reached and damaged brain cells - and Powers said families making those claims remain hopeful. The court has given no timetable for a ruling.
But Thursday's rulings clearly gave great credence to numerous large studies that have looked for but not found any link between the measles vaccine, other vaccines and autism.
"Hopefully, the determination by the special masters will help reassure parents that vaccines do not cause autism," the Department of Health and Human Services said in a statement that pledged to continue research into possible causes and better treatments.
"It's a great day for science, it's a great day for America's children when the court rules in favor of science," said Dr. Paul Offit, an infectious disease expert at the Children's Hospital of Philadelphia and developer of a vaccine for rotavirus.
"A choice not to get a vaccine is not a risk-free choice," Offit added, pointing to recent outbreaks of vaccine-preventable diseases that authorities suspect are partly due to delayed or rejected vaccinations.
Autism is best known for impairing a child's ability to communicate and interact. Recent data suggest a 10-fold increase in autism rates over the past decade, although it's unclear how much of the surge reflects better diagnosis.
Worry about a vaccine link first arose in 1998 when a British physician, Dr. Andrew Wakefield, published a medical journal article linking a particular type of autism and bowel disease to the measles vaccine. The study was soon discredited, and British medical authorities now are investigating professional misconduct charges against Wakefield.
Then came questions about thimerosal, a preservative that manufacturers began removing from all vaccines given to infants in 2001. Today it is present only in certain formulations of the flu shot.