Autistic children develop the condition around the age of two
The discovery could pave the way for treatments for the little understood condition.
A team from the Johns Hopkins Hospital in Baltimore found that families of children with autism have an unusually high incidence of such diseases, in particular rheumatoid arthritis.
The researchers stress that larger studies are needed to establish how strong the link is.
However, if it is proven, standard treatments such as steroids or injections of immunoglobulin may help in the management of the condition for some autistic children.
Increased incidence
Dr Anne Comi and colleagues sent questionnaires to the families of 61 children with and 46 children without autism.
They were asked if they suffered from autoimmune diseases such as rheumatoid arthritis, lupus, early-onset diabetes, multiple sclerosis and thyroid disorders.
Autoimmune diseases are caused by the body attacking itself - immune cells think the body's own tissue is foreign and seek to eradicate it.
The results showed that in 46% of the families of autistic children two or more members had autoimmune disorders and 21% of autistic children had at least one parent suffering from such a disorder.
This compared with 26% of normal children's families having such a disease and four per cent of parents.
Another finding was that 11% of children with autism had allergies compared with 39% of children without.
Further research
The finding supports earlier studies, Dr Comi told BBC News Online, and some researchers had even tried using autoimmune disease treatments on autistic children.
However, the research so far had been on a small-scale and more larger studies were needed, she said.
"It's going to be really important to look at larger numbers of patients and study them well - it may be useful in identifying subgroups of patients," she said.
"One of the reasons autism is so difficult is because it's so many things - it may be that what we call autism now is more than one condition, we just haven't figured that out yet."
The team published its findings in the Journal of Child Neurology.