The research published Wednesday in the online version of the journal Public Library of Science sought to test results of a 1998 study led by Dr Andrew Wakefield of the Royal Free Hospital in Britain which said there was a link between autism and this vaccine.
Wakefield, whose research also has appeared in Lancet, later officially pulled his findings.
Researchers at Columbia University in New York and at the Centers for Disease Control (CDC) looked for signs of genetic markers of the measles virus in intestinal tissue samples of 25 children with autism who also had intestinal troubles.
They compared the samples with 13 children of the same age who do not have autism but do have intestinal ailments.
The tissue was analyzed by three labs which did not know from which group of children the samples were taken.
"This study provides strong evidence against association of autism with persistent (measles virus) MV RNA in the GI tract or MMR exposure," the authors said.
Added Dr. Mady Hornig: "We found no relationship between the timing of MMR vaccine and the onset of either gastrointestinal complaints or autism."
The US Court of Federal Claims has been weighing a complaint by parents for over a year.
Parental concerns about potential vaccine risks by people who have opted not to have their children vaccinated have led to a major surge in measles outbreaks in the United States and Europe, the CDC says.
Measles kills some 250,000 people a year, mostly children in developing countries.
One child in 150 have autism or Asperger's in the United States, CDC data show.