But the researchers also admit they do not yet understand the reason for the possible link.
Suggestions include that heavy rainfall carries different chemicals from the atmosphere to ground level, or that children in rainy areas spend more time indoors watching TV or playing computers games, or coming in close contact with domestic chemicals.
Experts differ on how prevalent autism is in the population, but some estimate that up to one in 100 people could suffer from the condition.
The scientists, led by Dr Michael Waldman, from Cornell University in New York state, looked at children born in different parts of three American states, California, Oregon and Washington, between 1987 and 1999.
They then compared the annual rainfall that the children would have been exposed to in the first two years of their life.
The rates of autism later diagnosed "were positively related to the amount of precipitation these counties received from 1987 through 2001", according to the researchers.
"Similarly, focusing on (counties within) Oregon and California, autism prevalence was higher for (those children who) experienced relatively heavy precipitation when they were younger than 3 years."
As well as other explanations, "there is also the possibility that precipitation itself is more directly involved," according to the authors, whose findings were published in the Archives of Paediatrics & Adolescent Medicine journal.