The large Danish study looked at nearly 97,000 children born between 1997 and 2003.
Their mothers were screened to see if they had any infections, used antibiotics or had long periods of fever during their pregnancies.
Researchers found no association between Autism and minor infections, such as respiratory ailments, or urinary and genital infections.
But when it came to Influenza during pregnancy, the risk of being diagnosed with an Autism spectrum disorder before the age of three was twice as high for those children, compared to toddlers whose mothers did not have the flu during their pregnancies.
And if the mothers had a fever lasting more than a week while carrying a baby, that child had a three times greater risk of developing Autism than other children.
Researchers also found mothers who took antibiotics during their pregnancy had a small risk of having children with Autism.
Investigators say there may be statistical shortcomings in their data, and more research needs to be done to better understand the connection.