A study of almost 200,000 children found those with the developmental disability were more than two and a half times as likely to suffer a food intolerance.
The discovery adds to a growing body of evidence suggesting a disfunctioning immune system raises the risk of autism spectrum disorder (ASD).
Report author Professor Wei Bao, an epidemiologist at the University of Iowa, said: "It is possible the immunologic disruptions may have processes beginning early in life, which then influence brain development and social functioning, leading to the development of ASD."
The study analysed health information gathered by the National Health Interview Survey (NHIS), an annual survey of American households conducted by the US Centers for Disease Control and Prevention.
The children were aged three to 17 and the data was obtained between 1997 and 2016.
It found 11.25 per cent of children reportedly diagnosed with ASD have a food allergy, much more than the 4.25 per cent who are not diagnosed with ASD and have a food allergy.
The finding was observational so Prof Bao’s team could not establish intolerance as the cause of autism.
But previous studies have suggested possible links, including alterations in gut bacteria and increased production of antibodies and immune system overreactions.
These can lead to impaired brain function and neurodevelopmental abnormalities.
Prof Bao, whose research is published in JAMA Network Open, says the connections warrant further investigation.
He said: ‘We don’t know which comes first, food allergy or ASD.’
He adding a further study following children over many years since birth would be needed to establish this.
The latest study found 18.73 per cent of children with ASD suffered from respiratory allergies, while 12.08 per cent of children without it had them.
Meanwhile, 16.81 per cent of children with ASD had skin allergies, well above the 9.84 per cent of children who are not autistic.
Prof Bao said: ‘This indicates there could be a shared mechanism linking different types of allergic conditions to ASD.’
Autism has been suspected of being linked to such a food intolerance for more than 20 years.
A study two decades ago found a large proportion of autistic children, particularly those with late onset autism, responded well when fed a diet low in wheat, milk and other products linked to allergies.
But experts say diet is unlikely to be a cure.
There are around 700,000 people on the autism spectrum in the UK — more than one in 100.
Possible causes are genetic, viral or metabolic, with triggers including German measles.
It is also linked to epilepsy and there may be an association between difficult labour.