Here's yet another theory on a cause of autism. The theory: autism is caused by too much folic acid in early pregnancy.
The developing brain has more brain cells than it needs, expecting many of them to not work from the get-go or killed off somewhere along the way. Folic acid helps neurons live in early pregnancy as well as later. People with autism tend to have bigger brains, more brain cells, and poorer connections between the brain cells (there just isn't room for connections with all those extra cells). So, folic acid causes more brain cells to survive than ought to. This either leads to cramped neurons, or any fever at age 1 to 3 wipes out those cramped, stressed neurons, leaving brain damage. It's only folic acid in early pregnancy that is relevant here. Folic acid after birth may help or hurt autism, I have no reason to believe one way or the other.
Folic acid was recommended for women planning to become pregnant in 1992, and was added as a supplement to wheat flour in 1998. (Children conceived in 1998 would be 5 years old in 2004.) The rate of autism grew exponentially between 1992 and 1998, and saw a large spike at the end of the 1990s. However, it had already been growing exponentially for about a decade before 1992. That's the most obvious strike against this theory that I can see.
(Another theory I haven't done much research on is it's linked to ultrasounds.)
Update 2023: There have been studies.
The biggest known controllable factor seems to be folic acid and B12 during early pregnancy: get enough but not too much. Too much is worse than not enough. Oh and fathers sire kids when you're young.